[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/19775070/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/19780560/transformed.cor.cli.txt"

nPatients in clinical file=36, in cluster file=36, common to both=36
[1] "Reduce the number of clustering variables from 82 to 66."
[1] 66 36
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                26 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                26 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               21                15 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               21                15 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                30 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                30 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                33 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                33 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                28 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                28 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                33 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                33 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                24 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                24 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                24 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                24 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                29 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                29 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                29 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                30 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                30 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                24 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 31 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 31 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 32 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 32 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 32 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 32 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 27 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                 28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                 28 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 33 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 33 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 30 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 30 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 29 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 29 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 31 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 33 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 33 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 29 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 29 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                 30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                 30 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 30 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 30 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 25 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 25 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 24 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 33 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 33 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 31 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 31 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                32 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                32 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                14 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                14 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                33 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                33 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                26 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               13                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               13                23 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                31 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                31 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                16 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                32 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                32 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                32 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                32 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                26 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                26 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                33 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                33 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                18 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                18 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               19                17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               19                17 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 30 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 31 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 31 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                 28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                 28 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 27 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 33 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 33 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                15                 21 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                15                 21 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 23 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 31 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 31 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 32 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 32 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 29 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 29 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 26 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 26 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 30 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 28 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 28 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 32 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 32 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 33 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 33 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 31 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 31 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 21 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 21 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 31 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 31 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                21 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                21 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                21 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                21 
[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 36 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'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"                "33"                  
freq.contrast "33"               "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 36 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=28, 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  5 
[1] "table(vv)"
vv
T1 T2 T3 
19 12  5 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
T1 T2 T3 
19 12  5 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1 T2 T3 
19 12  5 
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 = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    7  3
  1P GAIN WILD-TYPE 11 15
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10                26 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                15 
$`1P GAIN MUTATED`
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       10.16        20.02         6.77         5.10        35.47         0.33 
TCGA-W5-AA34 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       18.25        23.05        24.36        13.45 

$`1P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        14.63        13.22        23.31        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       30.38         8.91        35.18        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 
       18.05         0.69         0.85         5.56        12.66        33.37 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.33              0.69 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            35.47             64.96 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            15.85             19.33 
[1] "0.3 - 35.5 (15.8)" "0.7 - 65.0 (19.3)"
[1] "hr=" "1.2"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  1P GAIN MUTATED         7        3         0        0         0         0
  1P GAIN WILD-TYPE      12        6         1        2         2         3
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7                12
  STAGE II                3                 6
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  1P GAIN MUTATED    7  3  0
  1P GAIN WILD-TYPE 12  9  5
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               7                12
  T2               3                 9
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    9  0
  1P GAIN WILD-TYPE 17  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    0
  1P GAIN WILD-TYPE   17    5
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0               9                17
  1               0                 5
[1] 2 2
[1] FALSE
D1V6, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   10  0
  1P GAIN WILD-TYPE 18  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     10    0
  1P GAIN WILD-TYPE   18    5
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              10                18
  1               0                 5
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    4  6
  1P GAIN WILD-TYPE 16 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      4    6
  1P GAIN WILD-TYPE   16   10
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               4                16
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  1P GAIN MUTATED                            0
  1P GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  1P GAIN MUTATED                                     0
  1P GAIN WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  1P GAIN MUTATED                                 10
  1P GAIN WILD-TYPE                               20
D1V8, multiclass
                                     clus
vv                                    1P GAIN MUTATED 1P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 10                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  1P GAIN MUTATED    7  3  0
  1P GAIN WILD-TYPE 21  2  3
D1V9, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               7                21
  R1               3                 2
  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
  1P GAIN MUTATED       1                         1     8
  1P GAIN WILD-TYPE     2                         1    23
D1V10, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   8                23
[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 = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   12  9
  1Q GAIN WILD-TYPE  6  9
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               21                15 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                9                 9 
$`1Q GAIN MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2Q 
       14.63        23.31        10.16        20.02         6.77         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        40.11        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-WD-A7RX TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
        0.33        35.18        18.25         0.69        12.66        23.05 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y8 
       24.36        33.37        13.45 

$`1Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O 
       11.15        13.22        64.96        20.88        63.75        21.04 
TCGA-W5-AA2U TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A 
       20.61        46.09        31.69         5.59        18.05         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        17.06         3.22 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.33              0.85 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            48.82             64.96 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            18.25             18.05 
[1] "0.3 - 48.8 (18.2)" "0.8 - 65.0 (18.1)"
[1] "hr=" "1.1"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  1Q GAIN MUTATED        10        7         0        0         2         2
  1Q GAIN WILD-TYPE       9        2         1        2         0         1
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                10                 9
  STAGE II                7                 2
  STAGE III               0                 1
  STAGE IV                0                 2
  STAGE IVA               2                 0
  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
  1Q GAIN MUTATED   10  9  2
  1Q GAIN WILD-TYPE  9  3  3
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              10                 9
  T2               9                 3
  T3               2                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   14  4
  1Q GAIN WILD-TYPE 12  1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     14    4
  1Q GAIN WILD-TYPE   12    1
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              14                12
  1               4                 1
[1] 2 2
[1] FALSE
D2V6, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   18  2
  1Q GAIN WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    2
  1Q GAIN WILD-TYPE   10    3
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              18                10
  1               2                 3
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   11 10
  1Q GAIN WILD-TYPE  9  6
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     11   10
  1Q GAIN WILD-TYPE    9    6
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              11                 9
  MALE                10                 6
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  1Q GAIN MUTATED                            0
  1Q GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  1Q GAIN MUTATED                                     2
  1Q GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  1Q GAIN MUTATED                                 19
  1Q GAIN WILD-TYPE                               11
D2V8, multiclass
                                     clus
vv                                    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 19                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  1Q GAIN MUTATED   15  4  2
  1Q GAIN WILD-TYPE 13  1  1
D2V9, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              15                13
  R1               4                 1
  RX               2                 1
[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
  1Q GAIN MUTATED       1                         1    19
  1Q GAIN WILD-TYPE     2                         1    12
D2V10, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  19                12
[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 = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    2  4
  2P GAIN WILD-TYPE 16 14
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                30 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                4                14 
$`2P GAIN MUTATED`
TCGA-W5-AA2G TCGA-W5-AA2Q TCGA-W5-AA2U TCGA-W5-AA2X TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       64.96         1.64        20.61         8.91         5.56        23.05 

$`2P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
        6.77        20.88        63.75        21.04        48.82        40.11 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        24.36        33.37        17.06        13.45         3.22 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             1.64              0.33 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            64.96             63.75 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            14.76             18.15 
[1] "1.6 - 65.0 (14.8)" "0.3 - 63.8 (18.1)"
[1] "hr=" "1.4"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  2P GAIN MUTATED         3        2         0        0         0         1
  2P GAIN WILD-TYPE      16        7         1        2         2         2
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                 3                16
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  2P GAIN MUTATED    3  3  0
  2P GAIN WILD-TYPE 16  9  5
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               3                16
  T2               3                 9
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  1
  2P GAIN WILD-TYPE 22  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    1
  2P GAIN WILD-TYPE   22    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               4                22
  1               1                 4
[1] 2 2
[1] FALSE
D3V6, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    5  1
  2P GAIN WILD-TYPE 23  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    1
  2P GAIN WILD-TYPE   23    4
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0               5                23
  1               1                 4
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    4  2
  2P GAIN WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      4    2
  2P GAIN WILD-TYPE   16   14
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               4                16
  MALE                 2                14
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  2P GAIN MUTATED                            0
  2P GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  2P GAIN MUTATED                                     1
  2P GAIN WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  2P GAIN MUTATED                                  5
  2P GAIN WILD-TYPE                               25
D3V8, multiclass
                                     clus
vv                                    2P GAIN MUTATED 2P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 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
  2P GAIN MUTATED    5  0  1
  2P GAIN WILD-TYPE 23  5  2
D3V9, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               5                23
  R1               0                 5
  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
  2P GAIN MUTATED       1                         1     4
  2P GAIN WILD-TYPE     2                         1    27
D3V10, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   4                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(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    2  4
  2Q GAIN WILD-TYPE 16 14
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                6                30 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                14 
$`2Q GAIN MUTATED`
TCGA-W5-AA2G TCGA-W5-AA2Q TCGA-W5-AA2X TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
       64.96         1.64         8.91         5.56        12.66        23.05 

$`2Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
        6.77        20.88        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       20.61        30.38         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        0.85        24.36        33.37        17.06        13.45         3.22 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             1.64              0.33 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            64.96             63.75 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           10.785            19.135 
[1] "1.6 - 65.0 (10.8)" "0.3 - 63.8 (19.1)"
[1] "hr=" "1.5"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  2Q GAIN MUTATED         2        2         0        0         1         1
  2Q GAIN WILD-TYPE      17        7         1        2         1         2
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                 2                17
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  2Q GAIN MUTATED    2  3  1
  2Q GAIN WILD-TYPE 17  9  4
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               2                17
  T2               3                 9
  T3               1                 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
  2Q GAIN MUTATED    3  2
  2Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    2
  2Q GAIN WILD-TYPE   23    3
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               3                23
  1               2                 3
[1] 2 2
[1] FALSE
D4V6, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    5  1
  2Q GAIN WILD-TYPE 23  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    1
  2Q GAIN WILD-TYPE   23    4
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0               5                23
  1               1                 4
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    4  2
  2Q GAIN WILD-TYPE 16 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      4    2
  2Q GAIN WILD-TYPE   16   14
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               4                16
  MALE                 2                14
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  2Q GAIN MUTATED                            0
  2Q GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  2Q GAIN MUTATED                                     1
  2Q GAIN WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  2Q GAIN MUTATED                                  5
  2Q GAIN WILD-TYPE                               25
D4V8, multiclass
                                     clus
vv                                    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 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
  2Q GAIN MUTATED    4  1  1
  2Q GAIN WILD-TYPE 24  4  2
D4V9, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               4                24
  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
  2Q GAIN MUTATED       1                         1     4
  2Q GAIN WILD-TYPE     2                         1    27
D4V10, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   4                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 = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 16 17
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                33 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                17 
$`3P GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 
       11.15        13.22         0.33 

$`3P GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       20.61        30.38         8.91         5.10        35.47        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.85         5.56        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.33              0.69 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            13.22             64.96 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            11.15             20.02 
[1] "0.3 - 13.2 (11.2)" "0.7 - 65.0 (20.0)"
[1] "hr=" "2.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  3P GAIN MUTATED         2        0         0        0         0         1
  3P GAIN WILD-TYPE      17        9         1        2         2         2
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                 2                17
  STAGE II                0                 9
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  3P GAIN MUTATED    2  0  1
  3P GAIN WILD-TYPE 17 12  4
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               2                17
  T2               0                12
  T3               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 24  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    1
  3P GAIN WILD-TYPE   24    4
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               2                24
  1               1                 4
[1] 2 2
[1] FALSE
D5V6, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 26  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2    1
  3P GAIN WILD-TYPE   26    4
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0               2                26
  1               1                 4
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED    1  2
  3P GAIN WILD-TYPE 19 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE   19   14
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                19
  MALE                 2                14
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  3P GAIN MUTATED                            1
  3P GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  3P GAIN MUTATED                                     0
  3P GAIN WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  3P GAIN MUTATED                                  2
  3P GAIN WILD-TYPE                               28
D5V8, multiclass
                                     clus
vv                                    3P GAIN MUTATED 3P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  3P GAIN MUTATED    3  0  0
  3P GAIN WILD-TYPE 25  5  3
D5V9, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               3                25
  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
  3P GAIN MUTATED       1                         0     2
  3P GAIN WILD-TYPE     2                         2    29
D5V10, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   2                29
[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 = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    5  3
  3Q GAIN WILD-TYPE 13 15
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                28 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                15 
$`3Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2X 
       11.15        13.22        23.31        10.16         6.77         8.91 
TCGA-W5-AA31 TCGA-W5-AA39 
        0.33         5.59 

$`3Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O 
       14.63        20.02        64.96        20.88        63.75        21.04 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z 
        1.64        48.82        40.11        20.61        30.38         5.10 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S 
       35.47        35.18        18.25        46.09        31.69        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        0.69         0.85         5.56        12.66        23.05        24.36 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45         3.22 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.33              0.69 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            23.31             64.96 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            9.535            20.745 
[1] "0.3 - 23.3 (9.5)"  "0.7 - 65.0 (20.7)"
[1] "hr=" "1.9"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  3Q GAIN MUTATED         4        2         0        0         0         2
  3Q GAIN WILD-TYPE      15        7         1        2         2         1
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                 4                15
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  3Q GAIN MUTATED    4  3  1
  3Q GAIN WILD-TYPE 15  9  4
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               4                15
  T2               3                 9
  T3               1                 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
  3Q GAIN MUTATED    6  2
  3Q GAIN WILD-TYPE 20  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    2
  3Q GAIN WILD-TYPE   20    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               6                20
  1               2                 3
[1] 2 2
[1] FALSE
D6V6, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    6  2
  3Q GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      6    2
  3Q GAIN WILD-TYPE   22    3
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0               6                22
  1               2                 3
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED    2  6
  3Q GAIN WILD-TYPE 18 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2    6
  3Q GAIN WILD-TYPE   18   10
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               2                18
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  3Q GAIN MUTATED                            1
  3Q GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  3Q GAIN MUTATED                                     2
  3Q GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  3Q GAIN MUTATED                                  5
  3Q GAIN WILD-TYPE                               25
D6V8, multiclass
                                     clus
vv                                    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  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
  3Q GAIN MUTATED    6  0  2
  3Q GAIN WILD-TYPE 22  5  1
D6V9, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               6                22
  R1               0                 5
  RX               2                 1
[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
  3Q GAIN MUTATED       2                         0     6
  3Q GAIN WILD-TYPE     1                         2    25
D6V10, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   6                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(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    1  2
  4P GAIN WILD-TYPE 17 16
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                33 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                2                16 
$`4P GAIN MUTATED`
TCGA-3X-AAVB TCGA-W5-AA39 TCGA-ZD-A8I3 
       13.22         5.59         5.56 

$`4P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        23.31        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S 
        0.33        35.18        18.25        46.09        31.69        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.69         0.85        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.56              0.33 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            13.22             64.96 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             5.59             20.02 
[1] "5.6 - 13.2 (5.6)"  "0.3 - 65.0 (20.0)"
[1] "hr=" "4.6"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  4P GAIN MUTATED         0        2         0        0         0         1
  4P GAIN WILD-TYPE      19        7         1        2         2         2
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                 0                19
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  4P GAIN MUTATED    0  2  1
  4P GAIN WILD-TYPE 19 10  4
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                19
  T2               2                10
  T3               1                 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
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 24  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   24    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                24
  1               1                 4
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 26  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   26    4
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0               2                26
  1               1                 4
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 18 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    1
  4P GAIN WILD-TYPE   18   15
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                18
  MALE                 1                15
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  4P GAIN MUTATED                            1
  4P GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  4P GAIN MUTATED                                     0
  4P GAIN WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  4P GAIN MUTATED                                  2
  4P GAIN WILD-TYPE                               28
D7V8, multiclass
                                     clus
vv                                    4P GAIN MUTATED 4P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  4P GAIN MUTATED    2  0  1
  4P GAIN WILD-TYPE 26  5  2
D7V9, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               2                26
  R1               0                 5
  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
  4P GAIN MUTATED       1                         0     2
  4P GAIN WILD-TYPE     2                         2    29
D7V10, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   2                29
[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 = 5P GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    7  5
  5P GAIN WILD-TYPE 11 13
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               12                24 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                5                13 
$`5P GAIN MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        13.22        23.31        10.16         6.77        64.96 
TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA39 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        5.10         0.33         5.59         5.56        23.05        24.36 

$`5P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-4G-AAZO TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
       11.15        20.02        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 
       48.82        40.11        20.61        30.38         8.91        35.47 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX 
       35.18        18.25        46.09        31.69        18.05         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        0.85        12.66        33.37        17.06        13.45         3.22 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.33              0.69 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            64.96             63.75 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           11.690            20.315 
[1] "0.3 - 65.0 (11.7)" "0.7 - 63.8 (20.3)"
[1] "hr=" "1"  
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  5P GAIN MUTATED         6        5         0        0         0         1
  5P GAIN WILD-TYPE      13        4         1        2         2         2
D8V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                 6                13
  STAGE II                5                 4
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  5P GAIN MUTATED    6  5  1
  5P GAIN WILD-TYPE 13  7  4
D8V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               6                13
  T2               5                 7
  T3               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    9  1
  5P GAIN WILD-TYPE 17  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      9    1
  5P GAIN WILD-TYPE   17    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0               9                17
  1               1                 4
[1] 2 2
[1] FALSE
D8V6, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   11  1
  5P GAIN WILD-TYPE 17  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11    1
  5P GAIN WILD-TYPE   17    4
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0              11                17
  1               1                 4
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED    7  5
  5P GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      7    5
  5P GAIN WILD-TYPE   13   11
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                13
  MALE                 5                11
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  5P GAIN MUTATED                            1
  5P GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  5P GAIN MUTATED                                     1
  5P GAIN WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  5P GAIN MUTATED                                 10
  5P GAIN WILD-TYPE                               20
D8V8, multiclass
                                     clus
vv                                    5P GAIN MUTATED 5P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 10                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  5P GAIN MUTATED    9  2  1
  5P GAIN WILD-TYPE 19  3  2
D8V9, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0               9                19
  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
  5P GAIN MUTATED       2                         1     9
  5P GAIN WILD-TYPE     1                         1    22
D8V10, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   9                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(9) Variable = 5Q GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    7  5
  5Q GAIN WILD-TYPE 11 13
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                24 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                5                13 
$`5Q GAIN MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        13.22        23.31        10.16         6.77        64.96 
TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA39 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        5.10         0.33         5.59         5.56        23.05        24.36 

$`5Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-4G-AAZO TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
       11.15        20.02        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 
       48.82        40.11        20.61        30.38         8.91        35.47 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX 
       35.18        18.25        46.09        31.69        18.05         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        0.85        12.66        33.37        17.06        13.45         3.22 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.33              0.69 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            64.96             63.75 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           11.690            20.315 
[1] "0.3 - 65.0 (11.7)" "0.7 - 63.8 (20.3)"
[1] "hr=" "1"  
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  5Q GAIN MUTATED         6        5         0        0         0         1
  5Q GAIN WILD-TYPE      13        4         1        2         2         2
D9V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                 6                13
  STAGE II                5                 4
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  5Q GAIN MUTATED    6  5  1
  5Q GAIN WILD-TYPE 13  7  4
D9V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               6                13
  T2               5                 7
  T3               1                 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
  5Q GAIN MUTATED    9  1
  5Q GAIN WILD-TYPE 17  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      9    1
  5Q GAIN WILD-TYPE   17    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0               9                17
  1               1                 4
[1] 2 2
[1] FALSE
D9V6, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   11  1
  5Q GAIN WILD-TYPE 17  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11    1
  5Q GAIN WILD-TYPE   17    4
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0              11                17
  1               1                 4
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    7  5
  5Q GAIN WILD-TYPE 13 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      7    5
  5Q GAIN WILD-TYPE   13   11
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               7                13
  MALE                 5                11
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  5Q GAIN MUTATED                            1
  5Q GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  5Q GAIN MUTATED                                     1
  5Q GAIN WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  5Q GAIN MUTATED                                 10
  5Q GAIN WILD-TYPE                               20
D9V8, multiclass
                                     clus
vv                                    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 10                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  5Q GAIN MUTATED    9  2  1
  5Q GAIN WILD-TYPE 19  3  2
D9V9, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0               9                19
  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
  5Q GAIN MUTATED       2                         1     9
  5Q GAIN WILD-TYPE     1                         1    22
D9V10, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   9                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(10) Variable = 6P GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  4
  6P GAIN WILD-TYPE 15 14
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                7                29 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                14 
$`6P GAIN MUTATED`
TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2X TCGA-W5-AA31 TCGA-W5-AA39 TCGA-ZH-A8Y2 
        6.77         1.64         8.91         0.33         5.59        23.05 
TCGA-ZH-A8Y4 
       24.36 

$`6P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
       64.96        20.88        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 
       20.61        30.38         5.10        35.47        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       46.09        31.69        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        33.37        17.06        13.45         3.22 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.33              0.69 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            24.36             64.96 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             6.77             20.02 
[1] "0.3 - 24.4 (6.8)"  "0.7 - 65.0 (20.0)"
[1] "hr=" "2.7"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  6P GAIN MUTATED         4        2         0        0         0         1
  6P GAIN WILD-TYPE      15        7         1        2         2         2
D10V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 4                15
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  6P GAIN MUTATED    4  3  0
  6P GAIN WILD-TYPE 15  9  5
D10V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                15
  T2               3                 9
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    5  1
  6P GAIN WILD-TYPE 21  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5    1
  6P GAIN WILD-TYPE   21    4
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               5                21
  1               1                 4
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    6  1
  6P GAIN WILD-TYPE 22  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      6    1
  6P GAIN WILD-TYPE   22    4
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               6                22
  1               1                 4
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED    1  6
  6P GAIN WILD-TYPE 19 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      1    6
  6P GAIN WILD-TYPE   19   10
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               1                19
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  6P GAIN MUTATED                            0
  6P GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  6P GAIN MUTATED                                     1
  6P GAIN WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  6P GAIN MUTATED                                  6
  6P GAIN WILD-TYPE                               24
D10V8, multiclass
                                     clus
vv                                    6P GAIN MUTATED 6P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 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
  6P GAIN MUTATED    4  1  2
  6P GAIN WILD-TYPE 24  4  1
D10V9, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               4                24
  R1               1                 4
  RX               2                 1
[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
  6P GAIN MUTATED       0                         1     6
  6P GAIN WILD-TYPE     3                         1    25
D10V10, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   6                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 7P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    2  5
  7P GAIN WILD-TYPE 16 13
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                7                29 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                13 
$`7P GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2O TCGA-W5-AA2U TCGA-W5-AA2X TCGA-ZH-A8Y2 
       13.22        23.31        21.04        20.61         8.91        23.05 
TCGA-ZH-A8Y4 
       24.36 

$`7P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2W 
       20.88        63.75         1.64        48.82        40.11        30.38 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 
        5.10        35.47         0.33        35.18        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        33.37        17.06        13.45         3.22 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             8.91              0.33 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            24.36             64.96 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            21.04             17.06 
[1] "8.9 - 24.4 (21.0)" "0.3 - 65.0 (17.1)"
[1] "hr=" "1.8"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  7P GAIN MUTATED         5        0         0        0         0         2
  7P GAIN WILD-TYPE      14        9         1        2         2         1
D11V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 5                14
  STAGE II                0                 9
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  7P GAIN MUTATED    5  1  1
  7P GAIN WILD-TYPE 14 11  4
D11V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               5                14
  T2               1                11
  T3               1                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  2
  7P GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    2
  7P GAIN WILD-TYPE   22    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               4                22
  1               2                 3
[1] 2 2
[1] FALSE
D11V6, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    5  2
  7P GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      5    2
  7P GAIN WILD-TYPE   23    3
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0               5                23
  1               2                 3
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4  3
  7P GAIN WILD-TYPE 16 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4    3
  7P GAIN WILD-TYPE   16   13
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               4                16
  MALE                 3                13
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  7P GAIN MUTATED                            1
  7P GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  7P GAIN MUTATED                                     2
  7P GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  7P GAIN MUTATED                                  4
  7P GAIN WILD-TYPE                               26
D11V8, multiclass
                                     clus
vv                                    7P GAIN MUTATED 7P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 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
  7P GAIN MUTATED    5  1  1
  7P GAIN WILD-TYPE 23  4  2
D11V9, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0               5                23
  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
  7P GAIN MUTATED       0                         1     6
  7P GAIN WILD-TYPE     3                         1    25
D11V10, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   6                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(12) Variable = 7Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED    2  4
  7Q GAIN WILD-TYPE 16 14
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                30 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                14 
$`7Q GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2O TCGA-W5-AA2X TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
       13.22        23.31        21.04         8.91        23.05        24.36 

$`7Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        63.75         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        5.56        12.66        33.37        17.06        13.45         3.22 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             8.91              0.33 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            24.36             64.96 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           22.045            17.555 
[1] "8.9 - 24.4 (22.0)" "0.3 - 65.0 (17.6)"
[1] "hr=" "1.6"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  7Q GAIN MUTATED         4        0         0        0         0         2
  7Q GAIN WILD-TYPE      15        9         1        2         2         1
D12V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 4                15
  STAGE II                0                 9
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  7Q GAIN MUTATED    4  1  1
  7Q GAIN WILD-TYPE 15 11  4
D12V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               4                15
  T2               1                11
  T3               1                 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
  7Q GAIN MUTATED    3  2
  7Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    2
  7Q GAIN WILD-TYPE   23    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               3                23
  1               2                 3
[1] 2 2
[1] FALSE
D12V6, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    4  2
  7Q GAIN WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      4    2
  7Q GAIN WILD-TYPE   24    3
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0               4                24
  1               2                 3
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3  3
  7Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3    3
  7Q GAIN WILD-TYPE   17   13
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               3                17
  MALE                 3                13
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  7Q GAIN MUTATED                            1
  7Q GAIN WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  7Q GAIN MUTATED                                     2
  7Q GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  7Q GAIN MUTATED                                  3
  7Q GAIN WILD-TYPE                               27
D12V8, multiclass
                                     clus
vv                                    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 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
  7Q GAIN MUTATED    4  1  1
  7Q GAIN WILD-TYPE 24  4  2
D12V9, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0               4                24
  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
  7Q GAIN MUTATED       0                         1     5
  7Q GAIN WILD-TYPE     3                         1    26
D12V10, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   5                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 8P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    5  1
  8P GAIN WILD-TYPE 13 17
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                6                30 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                17 
$`8P GAIN MUTATED`
TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-ZH-A8Y5 
       23.31        10.16         6.77         8.91         5.10        33.37 

$`8P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        14.63        13.22        20.02        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 
       30.38        35.47         0.33        35.18        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        23.05        24.36        17.06        13.45         3.22 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             5.10              0.33 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            33.37             64.96 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            9.535            19.135 
[1] "5.1 - 33.4 (9.5)"  "0.3 - 65.0 (19.1)"
[1] "hr=" "2.2"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  8P GAIN MUTATED         2        2         0        0         0         2
  8P GAIN WILD-TYPE      17        7         1        2         2         1
D13V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                 2                17
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  8P GAIN MUTATED    2  3  1
  8P GAIN WILD-TYPE 17  9  4
D13V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               2                17
  T2               3                 9
  T3               1                 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
  8P GAIN MUTATED    4  2
  8P GAIN WILD-TYPE 22  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    2
  8P GAIN WILD-TYPE   22    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               4                22
  1               2                 3
[1] 2 2
[1] FALSE
D13V6, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    4  2
  8P GAIN WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      4    2
  8P GAIN WILD-TYPE   24    3
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0               4                24
  1               2                 3
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED    2  4
  8P GAIN WILD-TYPE 18 12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    4
  8P GAIN WILD-TYPE   18   12
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               2                18
  MALE                 4                12
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  8P GAIN MUTATED                            0
  8P GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  8P GAIN MUTATED                                     2
  8P GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  8P GAIN MUTATED                                  4
  8P GAIN WILD-TYPE                               26
D13V8, multiclass
                                     clus
vv                                    8P GAIN MUTATED 8P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 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
  8P GAIN MUTATED    4  1  1
  8P GAIN WILD-TYPE 24  4  2
D13V9, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               4                24
  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
  8P GAIN MUTATED       1                         0     5
  8P GAIN WILD-TYPE     2                         2    26
D13V10, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   5                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 = 8Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    8  4
  8Q GAIN WILD-TYPE 10 14
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               12                24 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                4                14 
$`8Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2R TCGA-W5-AA2T 
       11.15        23.31        10.16         6.77        48.82        40.11 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
        8.91         5.10        35.47         0.33        23.05        33.37 

$`8Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I 
       14.63        13.22        20.02        64.96        20.88        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA33 TCGA-W5-AA34 
       21.04         1.64        20.61        30.38        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        5.56        12.66        24.36        17.06        13.45         3.22 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.33              0.69 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            48.82             64.96 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            17.10             18.15 
[1] "0.3 - 48.8 (17.1)" "0.7 - 65.0 (18.1)"
[1] "hr=" "1.7"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  8Q GAIN MUTATED         7        3         0        0         0         2
  8Q GAIN WILD-TYPE      12        6         1        2         2         1
D14V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 7                12
  STAGE II                3                 6
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  8Q GAIN MUTATED    7  4  1
  8Q GAIN WILD-TYPE 12  8  4
D14V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               7                12
  T2               4                 8
  T3               1                 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
  8Q GAIN MUTATED    9  2
  8Q GAIN WILD-TYPE 17  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9    2
  8Q GAIN WILD-TYPE   17    3
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0               9                17
  1               2                 3
[1] 2 2
[1] FALSE
D14V6, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   10  2
  8Q GAIN WILD-TYPE 18  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10    2
  8Q GAIN WILD-TYPE   18    3
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              10                18
  1               2                 3
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5  7
  8Q GAIN WILD-TYPE 15  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5    7
  8Q GAIN WILD-TYPE   15    9
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               5                15
  MALE                 7                 9
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  8Q GAIN MUTATED                            0
  8Q GAIN WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  8Q GAIN MUTATED                                     2
  8Q GAIN WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  8Q GAIN MUTATED                                 10
  8Q GAIN WILD-TYPE                               20
D14V8, multiclass
                                     clus
vv                                    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 10                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  8Q GAIN MUTATED   10  1  1
  8Q GAIN WILD-TYPE 18  4  2
D14V9, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              10                18
  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
  8Q GAIN MUTATED       2                         1     9
  8Q GAIN WILD-TYPE     1                         1    22
D14V10, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   9                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(15) Variable = 10P GAIN MUTATION ANALYSIS
D15V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    4  1
  10P GAIN WILD-TYPE 14 17
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 31 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                 17 
$`10P GAIN MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2Q TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-ZH-A8Y5 
       11.15         1.64         5.10         0.33        33.37 

$`10P GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       14.63        13.22        23.31        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
       64.96        20.88        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 
       20.61        30.38         8.91        35.47        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        5.56        12.66        23.05        24.36        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.33               0.69 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             33.37              64.96 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              5.10              20.02 
[1] "0.3 - 33.4 (5.1)"  "0.7 - 65.0 (20.0)"
[1] "hr=" "1.2"
D15V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  10P GAIN MUTATED         2        2         0        0         0         1
  10P GAIN WILD-TYPE      17        7         1        2         2         2
D15V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                  2                 17
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  10P GAIN MUTATED    2  2  1
  10P GAIN WILD-TYPE 17 10  4
D15V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                2                 17
  T2                2                 10
  T3                1                  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
  10P GAIN MUTATED    4  1
  10P GAIN WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    1
  10P GAIN WILD-TYPE   22    4
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                4                 22
  1                1                  4
[1] 2 2
[1] FALSE
D15V6, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    4  1
  10P GAIN WILD-TYPE 24  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      4    1
  10P GAIN WILD-TYPE   24    4
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0                4                 24
  1                1                  4
[1] 2 2
[1] FALSE
D15V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    1  4
  10P GAIN WILD-TYPE 19 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    4
  10P GAIN WILD-TYPE   19   12
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 19
  MALE                  4                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  10P GAIN MUTATED                            0
  10P GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  10P GAIN MUTATED                                     0
  10P GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  10P GAIN MUTATED                                  5
  10P GAIN WILD-TYPE                               25
D15V8, multiclass
                                     clus
vv                                    10P GAIN MUTATED 10P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  10P GAIN MUTATED    4  1  0
  10P GAIN WILD-TYPE 24  4  3
D15V9, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                4                 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
  10P GAIN MUTATED       1                         0     4
  10P GAIN WILD-TYPE     2                         2    27
D15V10, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                 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(16) Variable = 11P GAIN MUTATION ANALYSIS
D16V1, survival
                    sevent
clus2                 0  1
  11P GAIN MUTATED    1  3
  11P GAIN WILD-TYPE 17 15
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 4                 32 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 15 
$`11P GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2X TCGA-ZH-A8Y2 
       11.15        13.22         8.91        23.05 

$`11P GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       20.61        30.38         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85         5.56        12.66        24.36        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              8.91               0.33 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             23.05              64.96 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            12.185             19.135 
[1] "8.9 - 23.1 (12.2)" "0.3 - 65.0 (19.1)"
[1] "hr=" "2.8"
D16V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  11P GAIN MUTATED         2        0         0        0         0         2
  11P GAIN WILD-TYPE      17        9         1        2         2         1
D16V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                  2                 17
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  11P GAIN MUTATED    2  1  1
  11P GAIN WILD-TYPE 17 11  4
D16V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                2                 17
  T2                1                 11
  T3                1                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    1  2
  11P GAIN WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1    2
  11P GAIN WILD-TYPE   25    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                1                 25
  1                2                  3
[1] 2 2
[1] FALSE
D16V6, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 26  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   26    3
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0                2                 26
  1                2                  3
[1] 2 2
[1] FALSE
D16V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    2  2
  11P GAIN WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      2    2
  11P GAIN WILD-TYPE   18   14
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  11P GAIN MUTATED                            1
  11P GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  11P GAIN MUTATED                                     1
  11P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  11P GAIN MUTATED                                  2
  11P GAIN WILD-TYPE                               28
D16V8, multiclass
                                     clus
vv                                    11P GAIN MUTATED 11P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  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
  11P GAIN MUTATED    3  0  1
  11P GAIN WILD-TYPE 25  5  2
D16V9, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0                3                 25
  R1                0                  5
  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
  11P GAIN MUTATED       1                         1     2
  11P GAIN WILD-TYPE     2                         1    29
D16V10, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    2                 29
[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(17) Variable = 11Q GAIN MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  11Q GAIN MUTATED    1  3
  11Q GAIN WILD-TYPE 17 15
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 4                 32 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 3                 15 
$`11Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2X TCGA-ZH-A8Y2 
       11.15        13.22         8.91        23.05 

$`11Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       20.61        30.38         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85         5.56        12.66        24.36        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              8.91               0.33 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             23.05              64.96 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.185             19.135 
[1] "8.9 - 23.1 (12.2)" "0.3 - 65.0 (19.1)"
[1] "hr=" "2.8"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  11Q GAIN MUTATED         2        0         0        0         0         2
  11Q GAIN WILD-TYPE      17        9         1        2         2         1
D17V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                  2                 17
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  11Q GAIN MUTATED    2  1  1
  11Q GAIN WILD-TYPE 17 11  4
D17V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                2                 17
  T2                1                 11
  T3                1                  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"
D17V5, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    1  2
  11Q GAIN WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      1    2
  11Q GAIN WILD-TYPE   25    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                1                 25
  1                2                  3
[1] 2 2
[1] FALSE
D17V6, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  2
  11Q GAIN WILD-TYPE 26  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    2
  11Q GAIN WILD-TYPE   26    3
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0                2                 26
  1                2                  3
[1] 2 2
[1] FALSE
D17V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    2  2
  11Q GAIN WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      2    2
  11Q GAIN WILD-TYPE   18   14
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  11Q GAIN MUTATED                            1
  11Q GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  11Q GAIN MUTATED                                     1
  11Q GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  11Q GAIN MUTATED                                  2
  11Q GAIN WILD-TYPE                               28
D17V8, multiclass
                                     clus
vv                                    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  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
  11Q GAIN MUTATED    3  0  1
  11Q GAIN WILD-TYPE 25  5  2
D17V9, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0                3                 25
  R1                0                  5
  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
  11Q GAIN MUTATED       1                         1     2
  11Q GAIN WILD-TYPE     2                         1    29
D17V10, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    2                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 12P GAIN MUTATION ANALYSIS
D18V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    4  5
  12P GAIN WILD-TYPE 14 13
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 9                 27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 13 
$`12P GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 
       11.15        10.16         6.77         8.91         5.10         0.33 
TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y4 
       18.25         5.56        24.36 

$`12P GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        13.22        23.31        20.02        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       30.38        35.47        35.18        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       18.05         0.69         0.85        12.66        23.05        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.33               0.69 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             24.36              64.96 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              8.91              20.88 
[1] "0.3 - 24.4 (8.9)"  "0.7 - 65.0 (20.9)"
[1] "hr=" "3.5"
D18V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  12P GAIN MUTATED         5        3         0        0         0         1
  12P GAIN WILD-TYPE      14        6         1        2         2         2
D18V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                  5                 14
  STAGE II                 3                  6
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  12P GAIN MUTATED    5  4  0
  12P GAIN WILD-TYPE 14  8  5
D18V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                5                 14
  T2                4                  8
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8  1
  12P GAIN WILD-TYPE 18  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    1
  12P GAIN WILD-TYPE   18    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                8                 18
  1                1                  4
[1] 2 2
[1] FALSE
D18V6, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    8  1
  12P GAIN WILD-TYPE 20  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      8    1
  12P GAIN WILD-TYPE   20    4
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0                8                 20
  1                1                  4
[1] 2 2
[1] FALSE
D18V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED    3  6
  12P GAIN WILD-TYPE 17 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3    6
  12P GAIN WILD-TYPE   17   10
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  6                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  12P GAIN MUTATED                            0
  12P GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  12P GAIN MUTATED                                     1
  12P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  12P GAIN MUTATED                                  8
  12P GAIN WILD-TYPE                               22
D18V8, multiclass
                                     clus
vv                                    12P GAIN MUTATED 12P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  12P GAIN MUTATED    6  2  1
  12P GAIN WILD-TYPE 22  3  2
D18V9, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0                6                 22
  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
  12P GAIN MUTATED       3                         0     6
  12P GAIN WILD-TYPE     0                         2    25
D18V10, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    3                  0
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    6                 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(19) Variable = 12Q GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    4  4
  12Q GAIN WILD-TYPE 14 14
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 8                 28 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                 14 
$`12Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA34 
       11.15        10.16         6.77         5.10         0.33        18.25 
TCGA-ZD-A8I3 TCGA-ZH-A8Y4 
        5.56        24.36 

$`12Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        13.22        23.31        20.02        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 
       30.38         8.91        35.47        35.18        46.09        31.69 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
        5.59        18.05         0.69         0.85        12.66        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45         3.22 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.33               0.69 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             24.36              64.96 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             8.465             20.745 
[1] "0.3 - 24.4 (8.5)"  "0.7 - 65.0 (20.7)"
[1] "hr=" "2.7"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  12Q GAIN MUTATED         5        3         0        0         0         0
  12Q GAIN WILD-TYPE      14        6         1        2         2         3
D19V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                  5                 14
  STAGE II                 3                  6
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  12Q GAIN MUTATED    5  3  0
  12Q GAIN WILD-TYPE 14  9  5
D19V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                5                 14
  T2                3                  9
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V5, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  0
  12Q GAIN WILD-TYPE 18  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    0
  12Q GAIN WILD-TYPE   18    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                8                 18
  1                0                  5
[1] 2 2
[1] FALSE
D19V6, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    8  0
  12Q GAIN WILD-TYPE 20  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      8    0
  12Q GAIN WILD-TYPE   20    5
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0                8                 20
  1                0                  5
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    3  5
  12Q GAIN WILD-TYPE 17 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      3    5
  12Q GAIN WILD-TYPE   17   11
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  5                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  12Q GAIN MUTATED                            0
  12Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  12Q GAIN MUTATED                                     0
  12Q GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  12Q GAIN MUTATED                                  8
  12Q GAIN WILD-TYPE                               22
D19V8, multiclass
                                     clus
vv                                    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  12Q GAIN MUTATED    6  2  0
  12Q GAIN WILD-TYPE 22  3  3
D19V9, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                6                 22
  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
  12Q GAIN MUTATED       3                         0     5
  12Q GAIN WILD-TYPE     0                         2    26
D19V10, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                  0
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    5                 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(20) Variable = 13Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    2  1
  13Q GAIN WILD-TYPE 16 17
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 3                 33 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 17 
$`13Q GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2X 
       13.22        23.31         8.91 

$`13Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       20.61        30.38         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.85         5.56        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              8.91               0.33 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             23.31              64.96 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.22              18.25 
[1] "8.9 - 23.3 (13.2)" "0.3 - 65.0 (18.2)"
[1] "hr=" "1.1"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  13Q GAIN MUTATED         1        0         0        0         0         2
  13Q GAIN WILD-TYPE      18        9         1        2         2         1
D20V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  1                 18
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  13Q GAIN MUTATED    1  1  1
  13Q GAIN WILD-TYPE 18 11  4
D20V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                1                 18
  T2                1                 11
  T3                1                  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"
D20V5, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  2
  13Q GAIN WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    2
  13Q GAIN WILD-TYPE   25    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                1                 25
  1                2                  3
[1] 2 2
[1] FALSE
D20V6, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    1  2
  13Q GAIN WILD-TYPE 27  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      1    2
  13Q GAIN WILD-TYPE   27    3
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0                1                 27
  1                2                  3
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    2  1
  13Q GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      2    1
  13Q GAIN WILD-TYPE   18   15
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  13Q GAIN MUTATED                            1
  13Q GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  13Q GAIN MUTATED                                     2
  13Q GAIN WILD-TYPE                                   2
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  13Q GAIN MUTATED                                  0
  13Q GAIN WILD-TYPE                               30
D20V8, multiclass
                                     clus
vv                                    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                2                  2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                   0                 30
[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
  13Q GAIN MUTATED    2  0  1
  13Q GAIN WILD-TYPE 26  5  2
D20V9, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0                2                 26
  R1                0                  5
  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
  13Q GAIN MUTATED       0                         0     3
  13Q GAIN WILD-TYPE     3                         2    28
D20V10, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 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(21) Variable = 15Q GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  4
  15Q GAIN WILD-TYPE 16 14
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 6                 30 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 4                 14 
$`15Q GAIN MUTATED`
TCGA-3X-AAVC TCGA-W5-AA2W TCGA-W5-AA2X TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       23.31        30.38         8.91        23.05        24.36        13.45 

$`15Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       40.11        20.61         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.85         5.56        12.66        33.37        17.06         3.22 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.91               0.33 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             30.38              64.96 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            23.180             17.555 
[1] "8.9 - 30.4 (23.2)" "0.3 - 65.0 (17.6)"
[1] "hr=" "1.4"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  15Q GAIN MUTATED         4        0         0        0         1         1
  15Q GAIN WILD-TYPE      15        9         1        2         1         2
D21V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  15Q GAIN MUTATED    4  2  0
  15Q GAIN WILD-TYPE 15 10  5
D21V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                4                 15
  T2                2                 10
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  2
  15Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   23    3
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                3                 23
  1                2                  3
[1] 2 2
[1] FALSE
D21V6, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    5  1
  15Q GAIN WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      5    1
  15Q GAIN WILD-TYPE   23    4
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0                5                 23
  1                1                  4
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  3
  15Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    3
  15Q GAIN WILD-TYPE   17   13
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  15Q GAIN MUTATED                            0
  15Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  15Q GAIN MUTATED                                     2
  15Q GAIN WILD-TYPE                                   2
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  15Q GAIN MUTATED                                  4
  15Q GAIN WILD-TYPE                               26
D21V8, multiclass
                                     clus
vv                                    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                2                  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
  15Q GAIN MUTATED    4  1  1
  15Q GAIN WILD-TYPE 24  4  2
D21V9, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                 24
  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
  15Q GAIN MUTATED       0                         1     5
  15Q GAIN WILD-TYPE     3                         1    26
D21V10, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    5                 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(22) Variable = 16P GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE 13 16
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 7                 29 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 16 
$`16P GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2Q TCGA-ZD-A8I3 
       13.22        23.31         6.77        64.96         1.64         5.56 
TCGA-ZH-A8Y1 
       12.66 

$`16P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2H TCGA-W5-AA2I 
       11.15        14.63        10.16        20.02        20.88        63.75 
TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X 
       21.04        48.82        40.11        20.61        30.38         8.91 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 
        5.10        35.47         0.33        35.18        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y2 
       31.69         5.59        18.05         0.69         0.85        23.05 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       24.36        33.37        17.06        13.45         3.22 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1.64               0.33 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             64.96              63.75 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             12.66              20.02 
[1] "1.6 - 65.0 (12.7)" "0.3 - 63.8 (20.0)"
[1] "hr=" "1.8"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  16P GAIN MUTATED         3        2         0        0         1         1
  16P GAIN WILD-TYPE      16        7         1        2         1         2
D22V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  16P GAIN MUTATED    3  2  2
  16P GAIN WILD-TYPE 16 10  3
D22V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                3                 16
  T2                2                 10
  T3                2                  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"
D22V5, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE 21  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    2
  16P GAIN WILD-TYPE   21    3
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                5                 21
  1                2                  3
[1] 2 2
[1] FALSE
D22V6, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    6  1
  16P GAIN WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      6    1
  16P GAIN WILD-TYPE   22    4
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0                6                 22
  1                1                  4
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED    5  2
  16P GAIN WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5    2
  16P GAIN WILD-TYPE   15   14
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 15
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  16P GAIN MUTATED                            1
  16P GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  16P GAIN MUTATED                                     1
  16P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  16P GAIN MUTATED                                  5
  16P GAIN WILD-TYPE                               25
D22V8, multiclass
                                     clus
vv                                    16P GAIN MUTATED 16P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  16P GAIN MUTATED    6  1  0
  16P GAIN WILD-TYPE 22  4  3
D22V9, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                6                 22
  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
  16P GAIN MUTATED       1                         0     6
  16P GAIN WILD-TYPE     2                         2    25
D22V10, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    6                 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(23) Variable = 16Q GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    4  1
  16Q GAIN WILD-TYPE 14 17
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 5                 31 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                 17 
$`16Q GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2G TCGA-ZD-A8I3 
       13.22        23.31         6.77        64.96         5.56 

$`16Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2H TCGA-W5-AA2I 
       11.15        14.63        10.16        20.02        20.88        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       21.04         1.64        48.82        40.11        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
        8.91         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       12.66        23.05        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              5.56               0.33 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             64.96              63.75 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             13.22              18.25 
[1] "5.6 - 65.0 (13.2)" "0.3 - 63.8 (18.2)"
[1] "hr=" "3.4"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  16Q GAIN MUTATED         3        1         0        0         0         1
  16Q GAIN WILD-TYPE      16        8         1        2         2         2
D23V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  16Q GAIN MUTATED    3  1  1
  16Q GAIN WILD-TYPE 16 11  4
D23V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                1                  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"
D23V5, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  1
  16Q GAIN WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    1
  16Q GAIN WILD-TYPE   22    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                4                 22
  1                1                  4
[1] 2 2
[1] FALSE
D23V6, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  1
  16Q GAIN WILD-TYPE 24  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    1
  16Q GAIN WILD-TYPE   24    4
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0                4                 24
  1                1                  4
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    4  1
  16Q GAIN WILD-TYPE 16 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      4    1
  16Q GAIN WILD-TYPE   16   15
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                4                 16
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  16Q GAIN MUTATED                            1
  16Q GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  16Q GAIN MUTATED                                     1
  16Q GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  16Q GAIN MUTATED                                  3
  16Q GAIN WILD-TYPE                               27
D23V8, multiclass
                                     clus
vv                                    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  16Q GAIN MUTATED    5  0  0
  16Q GAIN WILD-TYPE 23  5  3
D23V9, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0                5                 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
  16Q GAIN MUTATED       1                         0     4
  16Q GAIN WILD-TYPE     2                         2    27
D23V10, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                 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(24) Variable = 17P GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    0  3
  17P GAIN WILD-TYPE 18 15
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 33 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 15 
$`17P GAIN MUTATED`
TCGA-W5-AA2X TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        8.91         5.56        23.05 

$`17P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        40.11        20.61        30.38         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        0.33        35.18        18.25        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       18.05         0.69         0.85        12.66        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              5.56               0.33 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             23.05              64.96 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              8.91              18.25 
[1] "5.6 - 23.1 (8.9)"  "0.3 - 65.0 (18.2)"
[1] "hr=" "4.1"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  17P GAIN MUTATED         1        1         0        0         0         1
  17P GAIN WILD-TYPE      18        8         1        2         2         2
D24V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                  1                 18
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  17P GAIN MUTATED    1  2  0
  17P GAIN WILD-TYPE 18 10  5
D24V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                1                 18
  T2                2                 10
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V5, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    1  1
  17P GAIN WILD-TYPE 25  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      1    1
  17P GAIN WILD-TYPE   25    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                1                 25
  1                1                  4
[1] 2 2
[1] FALSE
D24V6, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  1
  17P GAIN WILD-TYPE 26  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    1
  17P GAIN WILD-TYPE   26    4
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0                2                 26
  1                1                  4
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    2  1
  17P GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    1
  17P GAIN WILD-TYPE   18   15
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  17P GAIN MUTATED                            0
  17P GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  17P GAIN MUTATED                                     1
  17P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  17P GAIN MUTATED                                  2
  17P GAIN WILD-TYPE                               28
D24V8, multiclass
                                     clus
vv                                    17P GAIN MUTATED 17P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  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
  17P GAIN MUTATED    2  0  1
  17P GAIN WILD-TYPE 26  5  2
D24V9, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                2                 26
  R1                0                  5
  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
  17P GAIN MUTATED       1                         1     1
  17P GAIN WILD-TYPE     2                         1    30
D24V10, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    1                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 17Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    1  6
  17Q GAIN WILD-TYPE 17 12
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 7                 29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 6                 12 
$`17Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2O TCGA-W5-AA2X TCGA-W5-AA31 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       11.15        21.04         8.91         0.33         5.56        23.05 
TCGA-ZH-A8Y4 
       24.36 

$`17Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       14.63        13.22        23.31        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       64.96        20.88        63.75         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 
       20.61        30.38         5.10        35.47        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        33.37        17.06        13.45         3.22 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.33               0.69 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             24.36              64.96 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             11.15              18.25 
[1] "0.3 - 24.4 (11.2)" "0.7 - 65.0 (18.2)"
[1] "hr=" "3.8"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  17Q GAIN MUTATED         5        1         0        0         0         1
  17Q GAIN WILD-TYPE      14        8         1        2         2         2
D25V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                  5                 14
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  17Q GAIN MUTATED    5  2  0
  17Q GAIN WILD-TYPE 14 10  5
D25V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                5                 14
  T2                2                 10
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V5, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    5  1
  17Q GAIN WILD-TYPE 21  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      5    1
  17Q GAIN WILD-TYPE   21    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                5                 21
  1                1                  4
[1] 2 2
[1] FALSE
D25V6, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    6  1
  17Q GAIN WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6    1
  17Q GAIN WILD-TYPE   22    4
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0                6                 22
  1                1                  4
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED    2  5
  17Q GAIN WILD-TYPE 18 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      2    5
  17Q GAIN WILD-TYPE   18   11
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  5                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  17Q GAIN MUTATED                            0
  17Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  17Q GAIN MUTATED                                     1
  17Q GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  17Q GAIN MUTATED                                  6
  17Q GAIN WILD-TYPE                               24
D25V8, multiclass
                                     clus
vv                                    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  17Q GAIN MUTATED    5  1  1
  17Q GAIN WILD-TYPE 23  4  2
D25V9, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0                5                 23
  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
  17Q GAIN MUTATED       2                         1     4
  17Q GAIN WILD-TYPE     1                         1    27
D25V10, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    4                 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(26) Variable = 18P GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    4  3
  18P GAIN WILD-TYPE 14 15
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                 29 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 15 
$`18P GAIN MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2T TCGA-W5-AA31 TCGA-W5-AA34 
       13.22        23.31         6.77        40.11         0.33        18.25 
TCGA-ZD-A8I3 
        5.56 

$`18P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        14.63        10.16        20.02        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W 
       63.75        21.04         1.64        48.82        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 
        8.91         5.10        35.47        35.18        46.09        31.69 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
        5.59        18.05         0.69         0.85        12.66        23.05 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       24.36        33.37        17.06        13.45         3.22 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.33               0.69 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             40.11              64.96 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             13.22              20.02 
[1] "0.3 - 40.1 (13.2)" "0.7 - 65.0 (20.0)"
[1] "hr=" "1.2"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  18P GAIN MUTATED         4        2         0        0         0         1
  18P GAIN WILD-TYPE      15        7         1        2         2         2
D26V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  18P GAIN MUTATED    4  2  1
  18P GAIN WILD-TYPE 15 10  4
D26V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                4                 15
  T2                2                 10
  T3                1                  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"
D26V5, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  1
  18P GAIN WILD-TYPE 20  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    1
  18P GAIN WILD-TYPE   20    4
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                6                 20
  1                1                  4
[1] 2 2
[1] FALSE
D26V6, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    6  1
  18P GAIN WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    1
  18P GAIN WILD-TYPE   22    4
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0                6                 22
  1                1                  4
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    5  2
  18P GAIN WILD-TYPE 15 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      5    2
  18P GAIN WILD-TYPE   15   14
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                5                 15
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  18P GAIN MUTATED                            1
  18P GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  18P GAIN MUTATED                                     1
  18P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  18P GAIN MUTATED                                  5
  18P GAIN WILD-TYPE                               25
D26V8, multiclass
                                     clus
vv                                    18P GAIN MUTATED 18P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  18P GAIN MUTATED    7  0  0
  18P GAIN WILD-TYPE 21  5  3
D26V9, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                7                 21
  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
  18P GAIN MUTATED       1                         0     6
  18P GAIN WILD-TYPE     2                         2    25
D26V10, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    6                 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(27) Variable = 18Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    3  3
  18Q GAIN WILD-TYPE 15 15
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                 30 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 15 
$`18Q GAIN MUTATED`
TCGA-4G-AAZT TCGA-W5-AA2T TCGA-W5-AA31 TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y5 
        6.77        40.11         0.33        18.25         5.56        33.37 

$`18Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       20.61        30.38         8.91         5.10        35.47        35.18 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        23.05        24.36        17.06        13.45         3.22 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.33               0.69 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             40.11              64.96 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            12.510             19.035 
[1] "0.3 - 40.1 (12.5)" "0.7 - 65.0 (19.0)"
[1] "hr=" "1.3"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  18Q GAIN MUTATED         3        2         0        0         0         1
  18Q GAIN WILD-TYPE      16        7         1        2         2         2
D27V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  18Q GAIN MUTATED    3  2  1
  18Q GAIN WILD-TYPE 16 10  4
D27V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                3                 16
  T2                2                 10
  T3                1                  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"
D27V5, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  1
  18Q GAIN WILD-TYPE 21  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE   21    4
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                 21
  1                1                  4
[1] 2 2
[1] FALSE
D27V6, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    5  1
  18Q GAIN WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE   23    4
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0                5                 23
  1                1                  4
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    3  3
  18Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      3    3
  18Q GAIN WILD-TYPE   17   13
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  18Q GAIN MUTATED                            0
  18Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  18Q GAIN MUTATED                                     0
  18Q GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  18Q GAIN MUTATED                                  6
  18Q GAIN WILD-TYPE                               24
D27V8, multiclass
                                     clus
vv                                    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  18Q GAIN MUTATED    6  0  0
  18Q GAIN WILD-TYPE 22  5  3
D27V9, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                6                 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
  18Q GAIN MUTATED       1                         0     5
  18Q GAIN WILD-TYPE     2                         2    26
D27V10, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    5                 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(28) Variable = 19P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    4  2
  19P GAIN WILD-TYPE 14 16
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 6                 30 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 2                 16 
$`19P GAIN MUTATED`
TCGA-3X-AAVB TCGA-4G-AAZT TCGA-W5-AA2W TCGA-W5-AA31 TCGA-W5-AA33 TCGA-ZH-A8Y2 
       13.22         6.77        30.38         0.33        35.18        23.05 

$`19P GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       11.15        14.63        23.31        10.16        20.02        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 
       20.61         8.91         5.10        35.47        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        24.36        33.37        17.06        13.45         3.22 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.33               0.69 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             35.18              64.96 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            18.135             18.150 
[1] "0.3 - 35.2 (18.1)" "0.7 - 65.0 (18.1)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  19P GAIN MUTATED         4        0         0        0         1         1
  19P GAIN WILD-TYPE      15        9         1        2         1         2
D28V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  19P GAIN MUTATED    4  1  1
  19P GAIN WILD-TYPE 15 11  4
D28V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                4                 15
  T2                1                 11
  T3                1                  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"
D28V5, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  2
  19P GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    2
  19P GAIN WILD-TYPE   23    3
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                3                 23
  1                2                  3
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    5  1
  19P GAIN WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      5    1
  19P GAIN WILD-TYPE   23    4
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0                5                 23
  1                1                  4
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED    3  3
  19P GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3    3
  19P GAIN WILD-TYPE   17   13
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  19P GAIN MUTATED                            1
  19P GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  19P GAIN MUTATED                                     0
  19P GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  19P GAIN MUTATED                                  5
  19P GAIN WILD-TYPE                               25
D28V8, multiclass
                                     clus
vv                                    19P GAIN MUTATED 19P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  19P GAIN MUTATED    6  0  0
  19P GAIN WILD-TYPE 22  5  3
D28V9, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                6                 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
  19P GAIN MUTATED       0                         1     5
  19P GAIN WILD-TYPE     3                         1    26
D28V10, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    5                 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(29) Variable = 19Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    4  2
  19Q GAIN WILD-TYPE 14 16
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 6                 30 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 16 
$`19Q GAIN MUTATED`
TCGA-3X-AAVB TCGA-4G-AAZT TCGA-W5-AA2W TCGA-W5-AA31 TCGA-W5-AA33 TCGA-ZH-A8Y2 
       13.22         6.77        30.38         0.33        35.18        23.05 

$`19Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       11.15        14.63        23.31        10.16        20.02        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 
       20.61         8.91         5.10        35.47        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        24.36        33.37        17.06        13.45         3.22 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.33               0.69 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             35.18              64.96 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            18.135             18.150 
[1] "0.3 - 35.2 (18.1)" "0.7 - 65.0 (18.1)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  19Q GAIN MUTATED         4        0         0        0         1         1
  19Q GAIN WILD-TYPE      15        9         1        2         1         2
D29V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  19Q GAIN MUTATED    4  1  1
  19Q GAIN WILD-TYPE 15 11  4
D29V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                4                 15
  T2                1                 11
  T3                1                  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"
D29V5, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    3  2
  19Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    2
  19Q GAIN WILD-TYPE   23    3
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                3                 23
  1                2                  3
[1] 2 2
[1] FALSE
D29V6, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    5  1
  19Q GAIN WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    1
  19Q GAIN WILD-TYPE   23    4
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0                5                 23
  1                1                  4
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED    3  3
  19Q GAIN WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3    3
  19Q GAIN WILD-TYPE   17   13
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  19Q GAIN MUTATED                            1
  19Q GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  19Q GAIN MUTATED                                     0
  19Q GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  19Q GAIN MUTATED                                  5
  19Q GAIN WILD-TYPE                               25
D29V8, multiclass
                                     clus
vv                                    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  19Q GAIN MUTATED    6  0  0
  19Q GAIN WILD-TYPE 22  5  3
D29V9, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                6                 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
  19Q GAIN MUTATED       0                         1     5
  19Q GAIN WILD-TYPE     3                         1    26
D29V10, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    5                 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(30) Variable = 20P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    6  5
  20P GAIN WILD-TYPE 12 13
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                11                 25 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 13 
$`20P GAIN MUTATED`
TCGA-3X-AAV9 TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA31 
       11.15         6.77         1.64         8.91        35.47         0.33 
TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y8 
       18.25         5.56        23.05        33.37        13.45 

$`20P GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       14.63        13.22        23.31        10.16        20.02        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        63.75        21.04        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       30.38         5.10        35.18        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 
       18.05         0.69         0.85        12.66        24.36        17.06 
TCGA-ZU-A8S4 
        3.22 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.33               0.69 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             35.47              64.96 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             11.15              20.61 
[1] "0.3 - 35.5 (11.2)" "0.7 - 65.0 (20.6)"
[1] "hr=" "1.6"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  20P GAIN MUTATED         7        2         0        0         0         2
  20P GAIN WILD-TYPE      12        7         1        2         2         1
D30V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  7                 12
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  20P GAIN MUTATED    7  3  1
  20P GAIN WILD-TYPE 12  9  4
D30V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                7                 12
  T2                3                  9
  T3                1                  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"
D30V5, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    8  2
  20P GAIN WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8    2
  20P GAIN WILD-TYPE   18    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                8                 18
  1                2                  3
[1] 2 2
[1] FALSE
D30V6, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    9  2
  20P GAIN WILD-TYPE 19  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      9    2
  20P GAIN WILD-TYPE   19    3
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0                9                 19
  1                2                  3
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED    3  8
  20P GAIN WILD-TYPE 17  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      3    8
  20P GAIN WILD-TYPE   17    8
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                3                 17
  MALE                  8                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  20P GAIN MUTATED                            0
  20P GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  20P GAIN MUTATED                                     1
  20P GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  20P GAIN MUTATED                                 10
  20P GAIN WILD-TYPE                               20
D30V8, multiclass
                                     clus
vv                                    20P GAIN MUTATED 20P GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  10                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 RX
  20P GAIN MUTATED   10  0  1
  20P GAIN WILD-TYPE 18  5  2
D30V9, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               10                 18
  R1                0                  5
  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
  20P GAIN MUTATED       2                         1     8
  20P GAIN WILD-TYPE     1                         1    23
D30V10, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    8                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 20Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    7  5
  20Q GAIN WILD-TYPE 11 13
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                12                 24 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 13 
$`20Q GAIN MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2X TCGA-W5-AA30 
       11.15        23.31         6.77         1.64         8.91        35.47 
TCGA-W5-AA31 TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y8 
        0.33        18.25         5.56        23.05        33.37        13.45 

$`20Q GAIN WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H 
       14.63        13.22        10.16        20.02        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       63.75        21.04        48.82        40.11        20.61        30.38 
TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
        5.10        35.18        46.09        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.69         0.85        12.66        24.36        17.06         3.22 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.33               0.69 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             35.47              64.96 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            12.300             20.315 
[1] "0.3 - 35.5 (12.3)" "0.7 - 65.0 (20.3)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  20Q GAIN MUTATED         8        2         0        0         0         2
  20Q GAIN WILD-TYPE      11        7         1        2         2         1
D31V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  8                 11
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  20Q GAIN MUTATED    8  3  1
  20Q GAIN WILD-TYPE 11  9  4
D31V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                8                 11
  T2                3                  9
  T3                1                  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"
D31V5, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    9  2
  20Q GAIN WILD-TYPE 17  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      9    2
  20Q GAIN WILD-TYPE   17    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0                9                 17
  1                2                  3
[1] 2 2
[1] FALSE
D31V6, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   10  2
  20Q GAIN WILD-TYPE 18  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     10    2
  20Q GAIN WILD-TYPE   18    3
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0               10                 18
  1                2                  3
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED    4  8
  20Q GAIN WILD-TYPE 16  8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      4    8
  20Q GAIN WILD-TYPE   16    8
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                4                 16
  MALE                  8                  8
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  20Q GAIN MUTATED                            0
  20Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  20Q GAIN MUTATED                                     2
  20Q GAIN WILD-TYPE                                   2
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  20Q GAIN MUTATED                                 10
  20Q GAIN WILD-TYPE                               20
D31V8, multiclass
                                     clus
vv                                    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                2                  2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  10                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 RX
  20Q GAIN MUTATED   11  0  1
  20Q GAIN WILD-TYPE 17  5  2
D31V9, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0               11                 17
  R1                0                  5
  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
  20Q GAIN MUTATED       2                         1     9
  20Q GAIN WILD-TYPE     1                         1    22
D31V10, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    9                 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(32) Variable = 21Q GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 16 17
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 3                 33 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 17 
$`21Q GAIN MUTATED`
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-ZH-A8Y1 
        6.77        64.96        12.66 

$`21Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       35.18        18.25        46.09        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.69         0.85         5.56        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              6.77               0.33 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             64.96              63.75 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             12.66              18.25 
[1] "6.8 - 65.0 (12.7)" "0.3 - 63.8 (18.2)"
[1] "hr=" "2.5"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  21Q GAIN MUTATED         2        0         0        0         1         0
  21Q GAIN WILD-TYPE      17        9         1        2         1         3
D32V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                  2                 17
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  21Q GAIN MUTATED    2  0  1
  21Q GAIN WILD-TYPE 17 12  4
D32V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                2                 17
  T2                0                 12
  T3                1                  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"
D32V5, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 24  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   24    4
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                2                 24
  1                1                  4
[1] 2 2
[1] FALSE
D32V6, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    3  0
  21Q GAIN WILD-TYPE 25  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    0
  21Q GAIN WILD-TYPE   25    5
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0                3                 25
  1                0                  5
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    2  1
  21Q GAIN WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      2    1
  21Q GAIN WILD-TYPE   18   15
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  21Q GAIN MUTATED                            0
  21Q GAIN WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  21Q GAIN MUTATED                                     0
  21Q GAIN WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  21Q GAIN MUTATED                                  3
  21Q GAIN WILD-TYPE                               27
D32V8, multiclass
                                     clus
vv                                    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  21Q GAIN MUTATED    2  1  0
  21Q GAIN WILD-TYPE 26  4  3
D32V9, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                2                 26
  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
  21Q GAIN MUTATED       0                         0     3
  21Q GAIN WILD-TYPE     3                         2    28
D32V10, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 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(33) Variable = 22Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  1
  22Q GAIN WILD-TYPE 14 17
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 31 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                 17 
$`22Q GAIN MUTATED`
TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA31 
       13.22        64.96         8.91        35.47         0.33 

$`22Q GAIN WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 
       20.61        30.38         5.10        35.18        18.25        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       31.69         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       12.66        23.05        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.33               0.69 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             64.96              63.75 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             13.22              18.25 
[1] "0.3 - 65.0 (13.2)" "0.7 - 63.8 (18.2)"
[1] "hr=" "3.6"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  22Q GAIN MUTATED         3        0         0        0         0         2
  22Q GAIN WILD-TYPE      16        9         1        2         2         1
D33V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  22Q GAIN MUTATED    3  1  1
  22Q GAIN WILD-TYPE 16 11  4
D33V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                1                  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"
D33V5, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  2
  22Q GAIN WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    2
  22Q GAIN WILD-TYPE   23    3
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                3                 23
  1                2                  3
[1] 2 2
[1] FALSE
D33V6, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    3  2
  22Q GAIN WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    2
  22Q GAIN WILD-TYPE   25    3
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0                3                 25
  1                2                  3
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    2  3
  22Q GAIN WILD-TYPE 18 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      2    3
  22Q GAIN WILD-TYPE   18   13
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                2                 18
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  22Q GAIN MUTATED                            1
  22Q GAIN WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  22Q GAIN MUTATED                                     1
  22Q GAIN WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  22Q GAIN MUTATED                                  3
  22Q GAIN WILD-TYPE                               27
D33V8, multiclass
                                     clus
vv                                    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  22Q GAIN MUTATED    4  0  1
  22Q GAIN WILD-TYPE 24  5  2
D33V9, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                4                 24
  R1                0                  5
  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
  22Q GAIN MUTATED       0                         0     5
  22Q GAIN WILD-TYPE     3                         2    26
D33V10, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    5                 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(34) Variable = 1P LOSS MUTATION ANALYSIS
D34V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    2  2
  1P LOSS WILD-TYPE 16 16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                4                32 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                16 
$`1P LOSS MUTATED`
TCGA-W5-AA2X TCGA-W6-AA0S TCGA-ZD-A8I3 TCGA-ZH-A8Y5 
        8.91        18.05         5.56        33.37 

$`1P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        40.11        20.61        30.38         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        0.33        35.18        18.25        46.09        31.69         5.59 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y6 
        0.69         0.85        12.66        23.05        24.36        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             5.56              0.33 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            33.37             64.96 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           13.480            19.135 
[1] "5.6 - 33.4 (13.5)" "0.3 - 65.0 (19.1)"
[1] "hr=" "1.5"
D34V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  1P LOSS MUTATED         1        1         0        0         0         2
  1P LOSS WILD-TYPE      18        8         1        2         2         1
D34V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                 1                18
  STAGE II                1                 8
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  1P LOSS MUTATED    1  2  1
  1P LOSS WILD-TYPE 18 10  4
D34V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               1                18
  T2               2                10
  T3               1                 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"
D34V5, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  2
  1P LOSS WILD-TYPE 24  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    2
  1P LOSS WILD-TYPE   24    3
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               2                24
  1               2                 3
[1] 2 2
[1] FALSE
D34V6, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    1  2
  1P LOSS WILD-TYPE 27  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      1    2
  1P LOSS WILD-TYPE   27    3
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0               1                27
  1               2                 3
[1] 2 2
[1] FALSE
D34V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED    2  2
  1P LOSS WILD-TYPE 18 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    2
  1P LOSS WILD-TYPE   18   14
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                18
  MALE                 2                14
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  1P LOSS MUTATED                            0
  1P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  1P LOSS MUTATED                                     1
  1P LOSS WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  1P LOSS MUTATED                                  3
  1P LOSS WILD-TYPE                               27
D34V8, multiclass
                                     clus
vv                                    1P LOSS MUTATED 1P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 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
  1P LOSS MUTATED    3  0  1
  1P LOSS WILD-TYPE 25  5  2
D34V9, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0               3                25
  R1               0                 5
  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
  1P LOSS MUTATED       1                         0     3
  1P LOSS WILD-TYPE     2                         2    28
D34V10, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   3                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(35) Variable = 3P LOSS MUTATION ANALYSIS
D35V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   10 12
  3P LOSS WILD-TYPE  8  6
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               22                14 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12                 6 
$`3P LOSS MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I 
       14.63        23.31        10.16        20.02         6.77        63.75 
TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA2Z 
       21.04        48.82        40.11        20.61         8.91         5.10 
TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       35.47        18.25        46.09        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y8 
        0.69         5.56        23.05        13.45 

$`3P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2W 
       11.15        13.22        64.96        20.88         1.64        30.38 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.33        35.18         0.85        12.66        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.69              0.33 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            63.75             64.96 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           19.135            15.140 
[1] "0.7 - 63.8 (19.1)" "0.3 - 65.0 (15.1)"
[1] "hr=" "1.1"
D35V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  3P LOSS MUTATED        12        8         0        1         0         1
  3P LOSS WILD-TYPE       7        1         1        1         2         2
D35V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                12                 7
  STAGE II                8                 1
  STAGE III               0                 1
  STAGE IV                1                 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
  3P LOSS MUTATED   12  9  1
  3P LOSS WILD-TYPE  7  3  4
D35V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1              12                 7
  T2               9                 3
  T3               1                 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"
D35V5, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   18  1
  3P LOSS WILD-TYPE  8  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     18    1
  3P LOSS WILD-TYPE    8    4
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              18                 8
  1               1                 4
[1] 2 2
[1] FALSE
D35V6, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   18  2
  3P LOSS WILD-TYPE 10  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     18    2
  3P LOSS WILD-TYPE   10    3
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0              18                10
  1               2                 3
[1] 2 2
[1] FALSE
D35V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   14  8
  3P LOSS WILD-TYPE  6  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     14    8
  3P LOSS WILD-TYPE    6    8
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              14                 6
  MALE                 8                 8
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  3P LOSS MUTATED                            0
  3P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  3P LOSS MUTATED                                     3
  3P LOSS WILD-TYPE                                   1
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  3P LOSS MUTATED                                 19
  3P LOSS WILD-TYPE                               11
D35V8, multiclass
                                     clus
vv                                    3P LOSS MUTATED 3P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               3                 1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 19                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  3P LOSS MUTATED   17  2  3
  3P LOSS WILD-TYPE 11  3  0
D35V9, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0              17                11
  R1               2                 3
  RX               3                 0
[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
  3P LOSS MUTATED       2                         1    19
  3P LOSS WILD-TYPE     1                         1    12
D35V10, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  19                12
[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(36) Variable = 3Q LOSS MUTATION ANALYSIS
D36V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    0  3
  3Q LOSS WILD-TYPE 18 15
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                33 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                15 
$`3Q LOSS MUTATED`
TCGA-W5-AA2T TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       40.11         5.56        23.05 

$`3Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        0.33        35.18        18.25        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       18.05         0.69         0.85        12.66        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             5.56              0.33 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            40.11             64.96 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            23.05             18.05 
[1] "5.6 - 40.1 (23.1)" "0.3 - 65.0 (18.1)"
[1] "hr=" "2"  
D36V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  3Q LOSS MUTATED         1        2         0        0         0         0
  3Q LOSS WILD-TYPE      18        7         1        2         2         3
D36V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                 1                18
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  3Q LOSS MUTATED    1  2  0
  3Q LOSS WILD-TYPE 18 10  5
D36V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               1                18
  T2               2                10
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V5, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  0
  3Q LOSS WILD-TYPE 24  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    0
  3Q LOSS WILD-TYPE   24    5
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               2                24
  1               0                 5
[1] 2 2
[1] FALSE
D36V6, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  0
  3Q LOSS WILD-TYPE 25  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE   25    5
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0               3                25
  1               0                 5
[1] 2 2
[1] FALSE
D36V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    3  0
  3Q LOSS WILD-TYPE 17 16
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      3    0
  3Q LOSS WILD-TYPE   17   16
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               3                17
  MALE                 0                16
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  3Q LOSS MUTATED                            0
  3Q LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  3Q LOSS MUTATED                                     0
  3Q LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  3Q LOSS MUTATED                                  3
  3Q LOSS WILD-TYPE                               27
D36V8, multiclass
                                     clus
vv                                    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  3Q LOSS MUTATED    3  0  0
  3Q LOSS WILD-TYPE 25  5  3
D36V9, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               3                25
  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
  3Q LOSS MUTATED       1                         1     1
  3Q LOSS WILD-TYPE     2                         1    30
D36V10, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   1                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 4P LOSS MUTATION ANALYSIS
D37V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    5  5
  4P LOSS WILD-TYPE 13 13
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                13 
$`4P LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVE TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2X TCGA-W5-AA31 
       11.15        10.16        21.04        48.82         8.91         0.33 
TCGA-W5-AA38 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       31.69        23.05        24.36        13.45 

$`4P LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        13.22        23.31        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       20.88        63.75         1.64        40.11        20.61        30.38 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 
        5.10        35.47        35.18        18.25        46.09         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 
       18.05         0.69         0.85         5.56        12.66        33.37 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.33              0.69 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            48.82             64.96 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           17.245            18.150 
[1] "0.3 - 48.8 (17.2)" "0.7 - 65.0 (18.1)"
[1] "hr=" "1.1"
D37V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  4P LOSS MUTATED         8        1         0        0         0         1
  4P LOSS WILD-TYPE      11        8         1        2         2         2
D37V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 8                11
  STAGE II                1                 8
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  4P LOSS MUTATED    8  2  0
  4P LOSS WILD-TYPE 11 10  5
D37V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               8                11
  T2               2                10
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V5, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    8  1
  4P LOSS WILD-TYPE 18  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      8    1
  4P LOSS WILD-TYPE   18    4
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               8                18
  1               1                 4
[1] 2 2
[1] FALSE
D37V6, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    9  1
  4P LOSS WILD-TYPE 19  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      9    1
  4P LOSS WILD-TYPE   19    4
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0               9                19
  1               1                 4
[1] 2 2
[1] FALSE
D37V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED    3  7
  4P LOSS WILD-TYPE 17  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    7
  4P LOSS WILD-TYPE   17    9
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                17
  MALE                 7                 9
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  4P LOSS MUTATED                            0
  4P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  4P LOSS MUTATED                                     1
  4P LOSS WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  4P LOSS MUTATED                                  9
  4P LOSS WILD-TYPE                               21
D37V8, multiclass
                                     clus
vv                                    4P LOSS MUTATED 4P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  9                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  4P LOSS MUTATED    8  1  1
  4P LOSS WILD-TYPE 20  4  2
D37V9, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               8                20
  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
  4P LOSS MUTATED       2                         1     7
  4P LOSS WILD-TYPE     1                         1    24
D37V10, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 1
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   7                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(38) Variable = 4Q LOSS MUTATION ANALYSIS
D38V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    7  6
  4Q LOSS WILD-TYPE 11 12
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               13                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                12 
$`4Q LOSS MUTATED`
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X 
       10.16        20.02        21.04        48.82        30.38         8.91 
TCGA-W5-AA31 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        0.33        31.69         5.59        18.05        23.05        24.36 
TCGA-ZH-A8Y8 
       13.45 

$`4Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        13.22        23.31         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2Z 
       20.88        63.75         1.64        40.11        20.61         5.10 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-WD-A7RX TCGA-YR-A95A 
       35.47        35.18        18.25        46.09         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        12.66        33.37        17.06         3.22 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.33              0.69 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            48.82             64.96 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            20.02             17.06 
[1] "0.3 - 48.8 (20.0)" "0.7 - 65.0 (17.1)"
[1] "hr=" "1"  
D38V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  4Q LOSS MUTATED         8        3         0        0         1         1
  4Q LOSS WILD-TYPE      11        6         1        2         1         2
D38V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 8                11
  STAGE II                3                 6
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  4Q LOSS MUTATED    8  5  0
  4Q LOSS WILD-TYPE 11  7  5
D38V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               8                11
  T2               5                 7
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V5, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   10  2
  4Q LOSS WILD-TYPE 16  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     10    2
  4Q LOSS WILD-TYPE   16    3
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              10                16
  1               2                 3
[1] 2 2
[1] FALSE
D38V6, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   11  1
  4Q LOSS WILD-TYPE 17  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     11    1
  4Q LOSS WILD-TYPE   17    4
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              11                17
  1               1                 4
[1] 2 2
[1] FALSE
D38V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    6  7
  4Q LOSS WILD-TYPE 14  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      6    7
  4Q LOSS WILD-TYPE   14    9
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               6                14
  MALE                 7                 9
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  4Q LOSS MUTATED                            0
  4Q LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  4Q LOSS MUTATED                                     1
  4Q LOSS WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  4Q LOSS MUTATED                                 12
  4Q LOSS WILD-TYPE                               18
D38V8, multiclass
                                     clus
vv                                    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 12                18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  4Q LOSS MUTATED    9  2  2
  4Q LOSS WILD-TYPE 19  3  1
D38V9, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0               9                19
  R1               2                 3
  RX               2                 1
[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
  4Q LOSS MUTATED       1                         1    11
  4Q LOSS WILD-TYPE     2                         1    20
D38V10, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  11                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 6P LOSS MUTATION ANALYSIS
D39V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    3  2
  6P LOSS WILD-TYPE 15 16
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                5                31 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                16 
$`6P LOSS MUTATED`
TCGA-W5-AA2O TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-ZH-A8Y8 
       21.04        18.25        31.69        18.05        13.45 

$`6P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R 
        6.77        64.96        20.88        63.75         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
        0.33        35.18        46.09         5.59         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        5.56        12.66        23.05        24.36        33.37        17.06 
TCGA-ZU-A8S4 
        3.22 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.45              0.33 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            31.69             64.96 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            18.25             17.06 
[1] "13.4 - 31.7 (18.2)" "0.3 - 65.0 (17.1)" 
[1] "hr=" "1.2"
D39V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  6P LOSS MUTATED         5        0         0        0         0         0
  6P LOSS WILD-TYPE      14        9         1        2         2         3
D39V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                 5                14
  STAGE II                0                 9
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  6P LOSS MUTATED    5  0  0
  6P LOSS WILD-TYPE 14 12  5
D39V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               5                14
  T2               0                12
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V5, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    5  0
  6P LOSS WILD-TYPE 21  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      5    0
  6P LOSS WILD-TYPE   21    5
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               5                21
  1               0                 5
[1] 2 2
[1] FALSE
D39V6, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    4  0
  6P LOSS WILD-TYPE 24  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    0
  6P LOSS WILD-TYPE   24    5
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0               4                24
  1               0                 5
[1] 2 2
[1] FALSE
D39V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    3  2
  6P LOSS WILD-TYPE 17 14
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      3    2
  6P LOSS WILD-TYPE   17   14
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               3                17
  MALE                 2                14
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  6P LOSS MUTATED                            0
  6P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  6P LOSS MUTATED                                     0
  6P LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  6P LOSS MUTATED                                  5
  6P LOSS WILD-TYPE                               25
D39V8, multiclass
                                     clus
vv                                    6P LOSS MUTATED 6P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  6P LOSS MUTATED    5  0  0
  6P LOSS WILD-TYPE 23  5  3
D39V9, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0               5                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
  6P LOSS MUTATED       0                         0     5
  6P LOSS WILD-TYPE     3                         2    26
D39V10, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   5                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(40) Variable = 6Q LOSS MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    8 12
  6Q LOSS WILD-TYPE 10  6
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               20                16 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               12                 6 
$`6Q LOSS MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O 
       14.63        13.22        20.02         6.77        63.75        21.04 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       40.11        20.61        30.38         5.10        35.47         0.33 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 
       18.25        46.09        31.69        18.05         0.69         5.56 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
       23.05        24.36 

$`6Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2Q 
       11.15        23.31        10.16        64.96        20.88         1.64 
TCGA-W5-AA2R TCGA-W5-AA2X TCGA-W5-AA33 TCGA-W5-AA39 TCGA-YR-A95A TCGA-ZH-A8Y1 
       48.82         8.91        35.18         5.59         0.85        12.66 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45         3.22 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.33              0.85 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            63.75             64.96 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           20.315            13.055 
[1] "0.3 - 63.8 (20.3)" "0.8 - 65.0 (13.1)"
[1] "hr=" "1.4"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  6Q LOSS MUTATED        11        6         0        1         1         1
  6Q LOSS WILD-TYPE       8        3         1        1         1         2
D40V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                11                 8
  STAGE II                6                 3
  STAGE III               0                 1
  STAGE IV                1                 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
  6Q LOSS MUTATED   11  7  2
  6Q LOSS WILD-TYPE  8  5  3
D40V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              11                 8
  T2               7                 5
  T3               2                 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"
D40V5, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   15  2
  6Q LOSS WILD-TYPE 11  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15    2
  6Q LOSS WILD-TYPE   11    3
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              15                11
  1               2                 3
[1] 2 2
[1] FALSE
D40V6, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   16  2
  6Q LOSS WILD-TYPE 12  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     16    2
  6Q LOSS WILD-TYPE   12    3
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0              16                12
  1               2                 3
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   14  6
  6Q LOSS WILD-TYPE  6 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     14    6
  6Q LOSS WILD-TYPE    6   10
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              14                 6
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  6Q LOSS MUTATED                            1
  6Q LOSS WILD-TYPE                          1
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  6Q LOSS MUTATED                                     1
  6Q LOSS WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  6Q LOSS MUTATED                                 18
  6Q LOSS WILD-TYPE                               12
D40V8, multiclass
                                     clus
vv                                    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        1                 1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 18                12
[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
  6Q LOSS MUTATED   16  3  1
  6Q LOSS WILD-TYPE 12  2  2
D40V9, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              16                12
  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
  6Q LOSS MUTATED       1                         1    18
  6Q LOSS WILD-TYPE     2                         1    13
D40V10, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  18                13
[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(41) Variable = 7P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    0  4
  7P LOSS WILD-TYPE 18 14
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                32 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                14 
$`7P LOSS MUTATED`
TCGA-W5-AA2T TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZU-A8S4 
       40.11         5.56        12.66         3.22 

$`7P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
        6.77        64.96        20.88        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       48.82        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        0.33        35.18        18.25        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       18.05         0.69         0.85        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       17.06        13.45 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             3.22              0.33 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            40.11             64.96 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            9.110            19.135 
[1] "3.2 - 40.1 (9.1)"  "0.3 - 65.0 (19.1)"
[1] "hr=" "3.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  7P LOSS MUTATED         1        2         0        0         1         0
  7P LOSS WILD-TYPE      18        7         1        2         1         3
D41V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1                18
  STAGE II                2                 7
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  7P LOSS MUTATED    1  2  1
  7P LOSS WILD-TYPE 18 10  4
D41V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               1                18
  T2               2                10
  T3               1                 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"
D41V5, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    2  1
  7P LOSS WILD-TYPE 24  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    1
  7P LOSS WILD-TYPE   24    4
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               2                24
  1               1                 4
[1] 2 2
[1] FALSE
D41V6, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    3  0
  7P LOSS WILD-TYPE 25  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE   25    5
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3                25
  1               0                 5
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                 0  1
  7P LOSS MUTATED    3  1
  7P LOSS WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    1
  7P LOSS WILD-TYPE   17   15
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                17
  MALE                 1                15
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  7P LOSS MUTATED                            0
  7P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  7P LOSS MUTATED                                     0
  7P LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  7P LOSS MUTATED                                  4
  7P LOSS WILD-TYPE                               26
D41V8, multiclass
                                     clus
vv                                    7P LOSS MUTATED 7P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  7P LOSS MUTATED    3  1  0
  7P LOSS WILD-TYPE 25  4  3
D41V9, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               3                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
  7P LOSS MUTATED       1                         0     3
  7P LOSS WILD-TYPE     2                         2    28
D41V10, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   3                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(42) Variable = 7Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    1  3
  7Q LOSS WILD-TYPE 17 15
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4                32 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3                15 
$`7Q LOSS MUTATED`
TCGA-4G-AAZO TCGA-W5-AA2T TCGA-ZD-A8I3 TCGA-ZU-A8S4 
       20.02        40.11         5.56         3.22 

$`7Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        10.16         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       35.18        18.25        46.09        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.69         0.85        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       17.06        13.45 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             3.22              0.33 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            40.11             64.96 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            12.79             18.15 
[1] "3.2 - 40.1 (12.8)" "0.3 - 65.0 (18.1)"
[1] "hr=" "2.1"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  7Q LOSS MUTATED         1        3         0        0         0         0
  7Q LOSS WILD-TYPE      18        6         1        2         2         3
D42V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1                18
  STAGE II                3                 6
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  7Q LOSS MUTATED    1  3  0
  7Q LOSS WILD-TYPE 18  9  5
D42V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               1                18
  T2               3                 9
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V5, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  0
  7Q LOSS WILD-TYPE 23  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE   23    5
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3                23
  1               0                 5
[1] 2 2
[1] FALSE
D42V6, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  0
  7Q LOSS WILD-TYPE 25  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE   25    5
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3                25
  1               0                 5
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    3  1
  7Q LOSS WILD-TYPE 17 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    1
  7Q LOSS WILD-TYPE   17   15
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               3                17
  MALE                 1                15
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  7Q LOSS MUTATED                            0
  7Q LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  7Q LOSS MUTATED                                     0
  7Q LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  7Q LOSS MUTATED                                  4
  7Q LOSS WILD-TYPE                               26
D42V8, multiclass
                                     clus
vv                                    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  7Q LOSS MUTATED    3  1  0
  7Q LOSS WILD-TYPE 25  4  3
D42V9, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3                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
  7Q LOSS MUTATED       1                         0     3
  7Q LOSS WILD-TYPE     2                         2    28
D42V10, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   3                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(43) Variable = 8P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    6  4
  8P LOSS WILD-TYPE 12 14
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                26 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                14 
$`8P LOSS MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       11.15        64.96        21.04        35.47         0.33        35.18 
TCGA-W5-AA38 TCGA-WD-A7RX TCGA-ZH-A8Y2 TCGA-ZH-A8Y8 
       31.69         0.69        23.05        13.45 

$`8P LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       14.63        13.22        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        63.75         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 
       30.38         8.91         5.10        18.25        46.09         5.59 
TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       18.05         0.85         5.56        12.66        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.33              0.85 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            64.96             63.75 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           22.045            17.555 
[1] "0.3 - 65.0 (22.0)" "0.8 - 63.8 (17.6)"
[1] "hr=" "1.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  8P LOSS MUTATED         9        1         0        0         0         0
  8P LOSS WILD-TYPE      10        8         1        2         2         3
D43V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 9                10
  STAGE II                1                 8
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  8P LOSS MUTATED    9  1  0
  8P LOSS WILD-TYPE 10 11  5
D43V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               9                10
  T2               1                11
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V5, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    8  0
  8P LOSS WILD-TYPE 18  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      8    0
  8P LOSS WILD-TYPE   18    5
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               8                18
  1               0                 5
[1] 2 2
[1] FALSE
D43V6, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    9  0
  8P LOSS WILD-TYPE 19  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      9    0
  8P LOSS WILD-TYPE   19    5
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0               9                19
  1               0                 5
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4  6
  8P LOSS WILD-TYPE 16 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4    6
  8P LOSS WILD-TYPE   16   10
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE               4                16
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  8P LOSS MUTATED                            0
  8P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  8P LOSS MUTATED                                     0
  8P LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  8P LOSS MUTATED                                 10
  8P LOSS WILD-TYPE                               20
D43V8, multiclass
                                     clus
vv                                    8P LOSS MUTATED 8P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 10                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                R0 R1 RX
  8P LOSS MUTATED    9  0  1
  8P LOSS WILD-TYPE 19  5  2
D43V9, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0               9                19
  R1               0                 5
  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
  8P LOSS MUTATED       1                         1     8
  8P LOSS WILD-TYPE     2                         1    23
D43V10, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 2
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                   8                23
[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(44) Variable = 8Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    1  2
  8Q LOSS WILD-TYPE 17 16
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                3                33 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                16 
$`8Q LOSS MUTATED`
TCGA-W5-AA2O TCGA-W5-AA38 TCGA-WD-A7RX 
       21.04        31.69         0.69 

$`8Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO 
       11.15        14.63        13.22        23.31        10.16        20.02 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R 
        6.77        64.96        20.88        63.75         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S 
        0.33        35.18        18.25        46.09         5.59        18.05 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.85         5.56        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.69              0.33 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            31.69             64.96 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            21.04             18.05 
[1] "0.7 - 31.7 (21.0)" "0.3 - 65.0 (18.1)"
[1] "hr=" "1.6"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  8Q LOSS MUTATED         2        1         0        0         0         0
  8Q LOSS WILD-TYPE      17        8         1        2         2         3
D44V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                 2                17
  STAGE II                1                 8
  STAGE III               0                 1
  STAGE IV                0                 2
  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
  8Q LOSS MUTATED    2  1  0
  8Q LOSS WILD-TYPE 17 11  5
D44V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               2                17
  T2               1                11
  T3               0                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V5, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  0
  8Q LOSS WILD-TYPE 24  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    0
  8Q LOSS WILD-TYPE   24    5
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               2                24
  1               0                 5
[1] 2 2
[1] FALSE
D44V6, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  0
  8Q LOSS WILD-TYPE 26  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    0
  8Q LOSS WILD-TYPE   26    5
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0               2                26
  1               0                 5
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  1
  8Q LOSS WILD-TYPE 18 15
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    1
  8Q LOSS WILD-TYPE   18   15
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                18
  MALE                 1                15
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  8Q LOSS MUTATED                            0
  8Q LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  8Q LOSS MUTATED                                     0
  8Q LOSS WILD-TYPE                                   4
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  8Q LOSS MUTATED                                  3
  8Q LOSS WILD-TYPE                               27
D44V8, multiclass
                                     clus
vv                                    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               0                 4
  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
  8Q LOSS MUTATED    2  0  1
  8Q LOSS WILD-TYPE 26  5  2
D44V9, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               2                26
  R1               0                 5
  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
  8Q LOSS MUTATED       0                         0     3
  8Q LOSS WILD-TYPE     3                         2    28
D44V10, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                   3                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(45) Variable = 9P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    7 11
  9P LOSS WILD-TYPE 11  7
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               18                18 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               11                 7 
$`9P LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2I 
       11.15        23.31        10.16        20.02        64.96        63.75 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA38 
       40.11        20.61        30.38        35.47        18.25        31.69 
TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
        0.69         5.56        12.66        23.05        24.36        13.45 

$`9P LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q 
       14.63        13.22         6.77        20.88        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA36 
       48.82         8.91         5.10         0.33        35.18        46.09 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.59        18.05         0.85        33.37        17.06         3.22 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.69              0.33 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            64.96             48.82 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           21.830            13.925 
[1] "0.7 - 65.0 (21.8)" "0.3 - 48.8 (13.9)"
[1] "hr=" "1"  
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  9P LOSS MUTATED        11        5         0        0         2         0
  9P LOSS WILD-TYPE       8        4         1        2         0         3
D45V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                11                 8
  STAGE II                5                 4
  STAGE III               0                 1
  STAGE IV                0                 2
  STAGE IVA               2                 0
  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
  9P LOSS MUTATED   11  6  1
  9P LOSS WILD-TYPE  8  6  4
D45V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              11                 8
  T2               6                 6
  T3               1                 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"
D45V5, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   14  2
  9P LOSS WILD-TYPE 12  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     14    2
  9P LOSS WILD-TYPE   12    3
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              14                12
  1               2                 3
[1] 2 2
[1] FALSE
D45V6, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   17  0
  9P LOSS WILD-TYPE 11  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     17    0
  9P LOSS WILD-TYPE   11    5
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0              17                11
  1               0                 5
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   12  6
  9P LOSS WILD-TYPE  8 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     12    6
  9P LOSS WILD-TYPE    8   10
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              12                 8
  MALE                 6                10
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  9P LOSS MUTATED                            0
  9P LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  9P LOSS MUTATED                                     1
  9P LOSS WILD-TYPE                                   3
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  9P LOSS MUTATED                                 17
  9P LOSS WILD-TYPE                               13
D45V8, multiclass
                                     clus
vv                                    9P LOSS MUTATED 9P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               1                 3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 17                13
[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
  9P LOSS MUTATED   14  3  1
  9P LOSS WILD-TYPE 14  2  2
D45V9, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              14                14
  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
  9P LOSS MUTATED       3                         1    14
  9P LOSS WILD-TYPE     0                         1    17
D45V10, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 0
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  14                17
[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(46) Variable = 9Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    8 11
  9Q LOSS WILD-TYPE 10  7
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               19                17 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                 7 
$`9Q LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2I 
       11.15        23.31        10.16        20.02        64.96        63.75 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 
       40.11        20.61        35.47        35.18        18.25        31.69 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        0.69         0.85         5.56        12.66        23.05        24.36 
TCGA-ZH-A8Y8 
       13.45 

$`9Q LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q 
       14.63        13.22         6.77        20.88        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA36 
       48.82        30.38         8.91         5.10         0.33        46.09 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.59        18.05        33.37        17.06         3.22 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.69              0.33 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            64.96             48.82 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            20.61             14.63 
[1] "0.7 - 65.0 (20.6)" "0.3 - 48.8 (14.6)"
[1] "hr=" "1"  
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  9Q LOSS MUTATED        12        5         0        1         1         0
  9Q LOSS WILD-TYPE       7        4         1        1         1         3
D46V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                12                 7
  STAGE II                5                 4
  STAGE III               0                 1
  STAGE IV                1                 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
  9Q LOSS MUTATED   12  6  1
  9Q LOSS WILD-TYPE  7  6  4
D46V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              12                 7
  T2               6                 6
  T3               1                 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"
D46V5, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   15  1
  9Q LOSS WILD-TYPE 11  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     15    1
  9Q LOSS WILD-TYPE   11    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              15                11
  1               1                 4
[1] 2 2
[1] FALSE
D46V6, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   17  1
  9Q LOSS WILD-TYPE 11  4
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     17    1
  9Q LOSS WILD-TYPE   11    4
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0              17                11
  1               1                 4
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   11  8
  9Q LOSS WILD-TYPE  9  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     11    8
  9Q LOSS WILD-TYPE    9    8
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              11                 9
  MALE                 8                 8
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  9Q LOSS MUTATED                            0
  9Q LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  9Q LOSS MUTATED                                     2
  9Q LOSS WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  9Q LOSS MUTATED                                 17
  9Q LOSS WILD-TYPE                               13
D46V8, multiclass
                                     clus
vv                                    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 17                13
[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
  9Q LOSS MUTATED   14  4  1
  9Q LOSS WILD-TYPE 14  1  2
D46V9, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              14                14
  R1               4                 1
  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
  9Q LOSS MUTATED       3                         1    15
  9Q LOSS WILD-TYPE     0                         1    16
D46V10, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   3                 0
  BLACK OR AFRICAN AMERICAN               1                 1
  WHITE                                  15                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 10P LOSS MUTATION ANALYSIS
D47V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2  4
  10P LOSS WILD-TYPE 16 14
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 6                 30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 14 
$`10P LOSS MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2I TCGA-W5-AA2X TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
       13.22        23.31        63.75         8.91        23.05        24.36 

$`10P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        14.63        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        5.56        12.66        33.37        17.06        13.45         3.22 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              8.91               0.33 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             63.75              64.96 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            23.180             17.555 
[1] "8.9 - 63.8 (23.2)" "0.3 - 65.0 (17.6)"
[1] "hr=" "1"  
D47V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  10P LOSS MUTATED         4        0         0        0         0         2
  10P LOSS WILD-TYPE      15        9         1        2         2         1
D47V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  10P LOSS MUTATED    4  1  1
  10P LOSS WILD-TYPE 15 11  4
D47V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                4                 15
  T2                1                 11
  T3                1                  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"
D47V5, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3  2
  10P LOSS WILD-TYPE 23  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    2
  10P LOSS WILD-TYPE   23    3
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                3                 23
  1                2                  3
[1] 2 2
[1] FALSE
D47V6, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    4  2
  10P LOSS WILD-TYPE 24  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      4    2
  10P LOSS WILD-TYPE   24    3
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0                4                 24
  1                2                  3
[1] 2 2
[1] FALSE
D47V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED    3  3
  10P LOSS WILD-TYPE 17 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3    3
  10P LOSS WILD-TYPE   17   13
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                3                 17
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  10P LOSS MUTATED                            1
  10P LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  10P LOSS MUTATED                                     2
  10P LOSS WILD-TYPE                                   2
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  10P LOSS MUTATED                                  3
  10P LOSS WILD-TYPE                               27
D47V8, multiclass
                                     clus
vv                                    10P LOSS MUTATED 10P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                2                  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
  10P LOSS MUTATED    4  1  1
  10P LOSS WILD-TYPE 24  4  2
D47V9, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                4                 24
  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
  10P LOSS MUTATED       0                         1     5
  10P LOSS WILD-TYPE     3                         1    26
D47V10, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    5                 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(48) Variable = 10Q LOSS MUTATION ANALYSIS
D48V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    2  3
  10Q LOSS WILD-TYPE 16 15
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 31 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 15 
$`10Q LOSS MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVB TCGA-W5-AA2I TCGA-W5-AA30 TCGA-ZH-A8Y4 
       14.63        13.22        63.75        35.47        24.36 

$`10Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        23.31        10.16        20.02         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         8.91         5.10         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        5.56        12.66        23.05        33.37        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             13.22               0.33 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             63.75              64.96 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             24.36              18.05 
[1] "13.2 - 63.8 (24.4)" "0.3 - 65.0 (18.1)" 
[1] "hr=" "1.3"
D48V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  10Q LOSS MUTATED         3        1         0        0         0         1
  10Q LOSS WILD-TYPE      16        8         1        2         2         2
D48V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  10Q LOSS MUTATED    3  1  1
  10Q LOSS WILD-TYPE 16 11  4
D48V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                1                  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"
D48V5, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    3  1
  10Q LOSS WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3    1
  10Q LOSS WILD-TYPE   23    4
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                3                 23
  1                1                  4
[1] 2 2
[1] FALSE
D48V6, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    4  1
  10Q LOSS WILD-TYPE 24  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      4    1
  10Q LOSS WILD-TYPE   24    4
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0                4                 24
  1                1                  4
[1] 2 2
[1] FALSE
D48V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED    2  3
  10Q LOSS WILD-TYPE 18 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    3
  10Q LOSS WILD-TYPE   18   13
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                2                 18
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  10Q LOSS MUTATED                            1
  10Q LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  10Q LOSS MUTATED                                     0
  10Q LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  10Q LOSS MUTATED                                  4
  10Q LOSS WILD-TYPE                               26
D48V8, multiclass
                                     clus
vv                                    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  10Q LOSS MUTATED    4  1  0
  10Q LOSS WILD-TYPE 24  4  3
D48V9, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                4                 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
  10Q LOSS MUTATED       0                         0     5
  10Q LOSS WILD-TYPE     3                         2    26
D48V10, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    5                 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(49) Variable = 11P LOSS MUTATION ANALYSIS
D49V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    2  6
  11P LOSS WILD-TYPE 16 12
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 8                 28 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 12 
$`11P LOSS MUTATED`
TCGA-3X-AAVE TCGA-W5-AA2I TCGA-W5-AA2T TCGA-W5-AA31 TCGA-W5-AA34 TCGA-WD-A7RX 
       10.16        63.75        40.11         0.33        18.25         0.69 
TCGA-YR-A95A TCGA-ZH-A8Y4 
        0.85        24.36 

$`11P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U 
       64.96        20.88        21.04         1.64        48.82        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA36 
       30.38         8.91         5.10        35.47        35.18        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
       31.69         5.59        18.05         5.56        12.66        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45         3.22 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.33               1.64 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             63.75              64.96 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            14.205             19.035 
[1] "0.3 - 63.8 (14.2)" "1.6 - 65.0 (19.0)"
[1] "hr=" "1.8"
D49V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  11P LOSS MUTATED         4        3         0        1         0         0
  11P LOSS WILD-TYPE      15        6         1        1         2         3
D49V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 3                  6
  STAGE III                0                  1
  STAGE IV                 1                  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
  11P LOSS MUTATED    4  4  0
  11P LOSS WILD-TYPE 15  8  5
D49V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                4                 15
  T2                4                  8
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V5, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    6  0
  11P LOSS WILD-TYPE 20  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    0
  11P LOSS WILD-TYPE   20    5
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                6                 20
  1                0                  5
[1] 2 2
[1] FALSE
D49V6, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    6  1
  11P LOSS WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      6    1
  11P LOSS WILD-TYPE   22    4
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0                6                 22
  1                1                  4
[1] 2 2
[1] FALSE
D49V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED    3  5
  11P LOSS WILD-TYPE 17 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    5
  11P LOSS WILD-TYPE   17   11
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                 17
  MALE                  5                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  11P LOSS MUTATED                            0
  11P LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  11P LOSS MUTATED                                     1
  11P LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  11P LOSS MUTATED                                  7
  11P LOSS WILD-TYPE                               23
D49V8, multiclass
                                     clus
vv                                    11P LOSS MUTATED 11P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                   7                 23
[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
  11P LOSS MUTATED    5  2  1
  11P LOSS WILD-TYPE 23  3  2
D49V9, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                5                 23
  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
  11P LOSS MUTATED       1                         0     7
  11P LOSS WILD-TYPE     2                         2    24
D49V10, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    7                 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(50) Variable = 11Q LOSS MUTATION ANALYSIS
D50V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    3  6
  11Q LOSS WILD-TYPE 15 12
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 9                 27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 12 
$`11Q LOSS MUTATED`
TCGA-3X-AAVE TCGA-W5-AA2O TCGA-W5-AA2T TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA34 
       10.16        21.04        40.11        35.47         0.33        18.25 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y4 
        0.69         0.85        24.36 

$`11Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U 
       64.96        20.88        63.75         1.64        48.82        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 
       30.38         8.91         5.10        35.18        46.09        31.69 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
        5.59        18.05         5.56        12.66        23.05        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.33               1.64 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             40.11              64.96 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             18.25              18.05 
[1] "0.3 - 40.1 (18.2)" "1.6 - 65.0 (18.1)"
[1] "hr=" "2.1"
D50V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  11Q LOSS MUTATED         5        3         0        1         0         0
  11Q LOSS WILD-TYPE      14        6         1        1         2         3
D50V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                  5                 14
  STAGE II                 3                  6
  STAGE III                0                  1
  STAGE IV                 1                  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
  11Q LOSS MUTATED    5  4  0
  11Q LOSS WILD-TYPE 14  8  5
D50V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                5                 14
  T2                4                  8
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V5, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    7  0
  11Q LOSS WILD-TYPE 19  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    0
  11Q LOSS WILD-TYPE   19    5
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                7                 19
  1                0                  5
[1] 2 2
[1] FALSE
D50V6, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    7  1
  11Q LOSS WILD-TYPE 21  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      7    1
  11Q LOSS WILD-TYPE   21    4
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0                7                 21
  1                1                  4
[1] 2 2
[1] FALSE
D50V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED    3  6
  11Q LOSS WILD-TYPE 17 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    6
  11Q LOSS WILD-TYPE   17   10
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                 17
  MALE                  6                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  11Q LOSS MUTATED                            0
  11Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  11Q LOSS MUTATED                                     1
  11Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  11Q LOSS MUTATED                                  8
  11Q LOSS WILD-TYPE                               22
D50V8, multiclass
                                     clus
vv                                    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  11Q LOSS MUTATED    6  2  1
  11Q LOSS WILD-TYPE 22  3  2
D50V9, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                6                 22
  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
  11Q LOSS MUTATED       1                         0     8
  11Q LOSS WILD-TYPE     2                         2    23
D50V10, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    8                 23
[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(51) Variable = 12Q LOSS MUTATION ANALYSIS
D51V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE 16 17
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 33 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                 17 
$`12Q LOSS MUTATED`
TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA2X 
       13.22        64.96         8.91 

$`12Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       20.61        30.38         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       18.25        46.09        31.69         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
        0.85         5.56        12.66        23.05        24.36        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.91               0.33 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             64.96              63.75 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.22              18.25 
[1] "8.9 - 65.0 (13.2)" "0.3 - 63.8 (18.2)"
[1] "hr=" "2.6"
D51V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  12Q LOSS MUTATED         1        0         0        0         0         2
  12Q LOSS WILD-TYPE      18        9         1        2         2         1
D51V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                 18
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  12Q LOSS MUTATED    1  1  1
  12Q LOSS WILD-TYPE 18 11  4
D51V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                 18
  T2                1                 11
  T3                1                  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"
D51V5, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1  2
  12Q LOSS WILD-TYPE 25  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    2
  12Q LOSS WILD-TYPE   25    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                1                 25
  1                2                  3
[1] 2 2
[1] FALSE
D51V6, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    1  2
  12Q LOSS WILD-TYPE 27  3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    2
  12Q LOSS WILD-TYPE   27    3
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                1                 27
  1                2                  3
[1] 2 2
[1] FALSE
D51V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    2  1
  12Q LOSS WILD-TYPE 18 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   18   15
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 18
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  12Q LOSS MUTATED                            1
  12Q LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  12Q LOSS MUTATED                                     1
  12Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  12Q LOSS MUTATED                                  1
  12Q LOSS WILD-TYPE                               29
D51V8, multiclass
                                     clus
vv                                    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                   1                 29
[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
  12Q LOSS MUTATED    2  0  1
  12Q LOSS WILD-TYPE 26  5  2
D51V9, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0                2                 26
  R1                0                  5
  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
  12Q LOSS MUTATED       0                         0     3
  12Q LOSS WILD-TYPE     3                         2    28
D51V10, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 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(52) Variable = 13Q LOSS MUTATION ANALYSIS
D52V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    7  8
  13Q LOSS WILD-TYPE 11 10
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                15                 21 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 10 
$`13Q LOSS MUTATED`
TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
       10.16        64.96        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-WD-A7RX 
       20.61         5.10        35.18        18.25        31.69         0.69 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       12.66        13.45         3.22 

$`13Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA31 
       20.88         1.64        30.38         8.91        35.47         0.33 
TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       46.09         5.59        18.05         0.85         5.56        23.05 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       24.36        33.37        17.06 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.69               0.33 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             64.96              46.09 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             20.61              17.06 
[1] "0.7 - 65.0 (20.6)" "0.3 - 46.1 (17.1)"
[1] "hr=" "1.5"
D52V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  13Q LOSS MUTATED        10        4         0        0         1         0
  13Q LOSS WILD-TYPE       9        5         1        2         1         3
D52V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 10                  9
  STAGE II                 4                  5
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  13Q LOSS MUTATED   10  4  1
  13Q LOSS WILD-TYPE  9  8  4
D52V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               10                  9
  T2                4                  8
  T3                1                  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"
D52V5, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   12  1
  13Q LOSS WILD-TYPE 14  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     12    1
  13Q LOSS WILD-TYPE   14    4
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               12                 14
  1                1                  4
[1] 2 2
[1] FALSE
D52V6, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   13  0
  13Q LOSS WILD-TYPE 15  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     13    0
  13Q LOSS WILD-TYPE   15    5
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               13                 15
  1                0                  5
[1] 2 2
[1] FALSE
D52V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    9  6
  13Q LOSS WILD-TYPE 11 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      9    6
  13Q LOSS WILD-TYPE   11   10
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                9                 11
  MALE                  6                 10
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  13Q LOSS MUTATED                            0
  13Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  13Q LOSS MUTATED                                     0
  13Q LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  13Q LOSS MUTATED                                 15
  13Q LOSS WILD-TYPE                               15
D52V8, multiclass
                                     clus
vv                                    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  15                 15
[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
  13Q LOSS MUTATED   12  2  1
  13Q LOSS WILD-TYPE 16  3  2
D52V9, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               12                 16
  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
  13Q LOSS MUTATED       1                         0    14
  13Q LOSS WILD-TYPE     2                         2    17
D52V10, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                   14                 17
[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(53) Variable = 14Q LOSS MUTATION ANALYSIS
D53V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    6  7
  14Q LOSS WILD-TYPE 12 11
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 23 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 11 
$`14Q LOSS MUTATED`
TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2T TCGA-W5-AA2U 
       14.63        10.16        20.02         6.77        40.11        20.61 
TCGA-W5-AA30 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-WD-A7RX TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
       35.47        46.09        31.69         0.69        23.05        24.36 
TCGA-ZH-A8Y8 
       13.45 

$`14Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I 
       11.15        13.22        23.31        64.96        20.88        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z 
       21.04         1.64        48.82        30.38         8.91         5.10 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A 
        0.33        35.18        18.25         5.59        18.05         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        12.66        33.37        17.06         3.22 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.69               0.33 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             46.09              64.96 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             20.61              17.06 
[1] "0.7 - 46.1 (20.6)" "0.3 - 65.0 (17.1)"
[1] "hr=" "1"  
D53V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  14Q LOSS MUTATED         7        5         0        1         0         0
  14Q LOSS WILD-TYPE      12        4         1        1         2         3
D53V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  7                 12
  STAGE II                 5                  4
  STAGE III                0                  1
  STAGE IV                 1                  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
  14Q LOSS MUTATED    7  5  1
  14Q LOSS WILD-TYPE 12  7  4
D53V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                7                 12
  T2                5                  7
  T3                1                  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"
D53V5, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   10  0
  14Q LOSS WILD-TYPE 16  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     10    0
  14Q LOSS WILD-TYPE   16    5
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               10                 16
  1                0                  5
[1] 2 2
[1] FALSE
D53V6, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   11  1
  14Q LOSS WILD-TYPE 17  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     11    1
  14Q LOSS WILD-TYPE   17    4
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0               11                 17
  1                1                  4
[1] 2 2
[1] FALSE
D53V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    8  5
  14Q LOSS WILD-TYPE 12 11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8    5
  14Q LOSS WILD-TYPE   12   11
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                8                 12
  MALE                  5                 11
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  14Q LOSS MUTATED                            0
  14Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  14Q LOSS MUTATED                                     1
  14Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  14Q LOSS MUTATED                                 12
  14Q LOSS WILD-TYPE                               18
D53V8, multiclass
                                     clus
vv                                    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  12                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 R0 R1 RX
  14Q LOSS MUTATED   10  2  1
  14Q LOSS WILD-TYPE 18  3  2
D53V9, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               10                 18
  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
  14Q LOSS MUTATED       1                         1    11
  14Q LOSS WILD-TYPE     2                         1    20
D53V10, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   11                 20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 15Q LOSS MUTATION ANALYSIS
D54V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    4  1
  15Q LOSS WILD-TYPE 14 17
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 31 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                 17 
$`15Q LOSS MUTATED`
TCGA-3X-AAVB TCGA-W5-AA2G TCGA-W5-AA30 TCGA-W5-AA31 TCGA-ZU-A8S4 
       13.22        64.96        35.47         0.33         3.22 

$`15Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        23.31        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       20.88        63.75        21.04         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA34 
       20.61        30.38         8.91         5.10        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        5.56        12.66        23.05        24.36        33.37        17.06 
TCGA-ZH-A8Y8 
       13.45 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.33               0.69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             64.96              63.75 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             13.22              18.25 
[1] "0.3 - 65.0 (13.2)" "0.7 - 63.8 (18.2)"
[1] "hr=" "3.4"
D54V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  15Q LOSS MUTATED         4        0         0        0         0         1
  15Q LOSS WILD-TYPE      15        9         1        2         2         2
D54V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  15Q LOSS MUTATED    4  0  1
  15Q LOSS WILD-TYPE 15 12  4
D54V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                4                 15
  T2                0                 12
  T3                1                  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"
D54V5, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  1
  15Q LOSS WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    1
  15Q LOSS WILD-TYPE   23    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                3                 23
  1                1                  4
[1] 2 2
[1] FALSE
D54V6, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    3  1
  15Q LOSS WILD-TYPE 25  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    1
  15Q LOSS WILD-TYPE   25    4
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0                3                 25
  1                1                  4
[1] 2 2
[1] FALSE
D54V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    2  3
  15Q LOSS WILD-TYPE 18 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    3
  15Q LOSS WILD-TYPE   18   13
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                2                 18
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  15Q LOSS MUTATED                            1
  15Q LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  15Q LOSS MUTATED                                     0
  15Q LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  15Q LOSS MUTATED                                  4
  15Q LOSS WILD-TYPE                               26
D54V8, multiclass
                                     clus
vv                                    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  15Q LOSS MUTATED    5  0  0
  15Q LOSS WILD-TYPE 23  5  3
D54V9, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                5                 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
  15Q LOSS MUTATED       0                         0     5
  15Q LOSS WILD-TYPE     3                         2    26
D54V10, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    5                 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(55) Variable = 16P LOSS MUTATION ANALYSIS
D55V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    3  1
  16P LOSS WILD-TYPE 15 17
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 4                 32 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 17 
$`16P LOSS MUTATED`
TCGA-3X-AAVE TCGA-W5-AA30 TCGA-W5-AA38 TCGA-ZH-A8Y4 
       10.16        35.47        31.69        24.36 

$`16P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 
       40.11        20.61        30.38         8.91         5.10         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX 
       35.18        18.25        46.09         5.59        18.05         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85         5.56        12.66        23.05        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             10.16               0.33 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             35.47              64.96 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            28.025             17.555 
[1] "10.2 - 35.5 (28.0)" "0.3 - 65.0 (17.6)" 
[1] "hr=" "2.7"
D55V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  16P LOSS MUTATED         3        1         0        0         0         0
  16P LOSS WILD-TYPE      16        8         1        2         2         3
D55V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  16P LOSS MUTATED    3  1  0
  16P LOSS WILD-TYPE 16 11  5
D55V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V5, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  0
  16P LOSS WILD-TYPE 22  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    0
  16P LOSS WILD-TYPE   22    5
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                4                 22
  1                0                  5
[1] 2 2
[1] FALSE
D55V6, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    4  0
  16P LOSS WILD-TYPE 24  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    0
  16P LOSS WILD-TYPE   24    5
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0                4                 24
  1                0                  5
[1] 2 2
[1] FALSE
D55V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    1  3
  16P LOSS WILD-TYPE 19 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      1    3
  16P LOSS WILD-TYPE   19   13
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                1                 19
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  16P LOSS MUTATED                            0
  16P LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  16P LOSS MUTATED                                     0
  16P LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  16P LOSS MUTATED                                  4
  16P LOSS WILD-TYPE                               26
D55V8, multiclass
                                     clus
vv                                    16P LOSS MUTATED 16P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  16P LOSS MUTATED    3  1  0
  16P LOSS WILD-TYPE 25  4  3
D55V9, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                3                 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
  16P LOSS MUTATED       1                         0     3
  16P LOSS WILD-TYPE     2                         2    28
D55V10, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 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(56) Variable = 16Q LOSS MUTATION ANALYSIS
D56V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    4  3
  16Q LOSS WILD-TYPE 14 15
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 29 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 3                 15 
$`16Q LOSS MUTATED`
TCGA-3X-AAVE TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-ZH-A8Y1 
       10.16         5.10        35.47        18.25        31.69        12.66 
TCGA-ZH-A8Y4 
       24.36 

$`16Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        23.31        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R 
       64.96        20.88        63.75        21.04         1.64        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA31 TCGA-W5-AA33 
       40.11        20.61        30.38         8.91         0.33        35.18 
TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       46.09         5.59        18.05         0.69         0.85         5.56 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       23.05        33.37        17.06        13.45         3.22 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              5.10               0.33 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             35.47              64.96 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             18.25              18.05 
[1] "5.1 - 35.5 (18.2)" "0.3 - 65.0 (18.1)"
[1] "hr=" "1.1"
D56V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  16Q LOSS MUTATED         4        2         0        0         1         0
  16Q LOSS WILD-TYPE      15        7         1        2         1         3
D56V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  16Q LOSS MUTATED    4  2  1
  16Q LOSS WILD-TYPE 15 10  4
D56V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                4                 15
  T2                2                 10
  T3                1                  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"
D56V5, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    6  1
  16Q LOSS WILD-TYPE 20  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      6    1
  16Q LOSS WILD-TYPE   20    4
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                6                 20
  1                1                  4
[1] 2 2
[1] FALSE
D56V6, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  0
  16Q LOSS WILD-TYPE 21  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    0
  16Q LOSS WILD-TYPE   21    5
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0                7                 21
  1                0                  5
[1] 2 2
[1] FALSE
D56V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    4  3
  16Q LOSS WILD-TYPE 16 13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      4    3
  16Q LOSS WILD-TYPE   16   13
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                4                 16
  MALE                  3                 13
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  16Q LOSS MUTATED                            0
  16Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  16Q LOSS MUTATED                                     0
  16Q LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  16Q LOSS MUTATED                                  7
  16Q LOSS WILD-TYPE                               23
D56V8, multiclass
                                     clus
vv                                    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                   7                 23
[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
  16Q LOSS MUTATED    4  3  0
  16Q LOSS WILD-TYPE 24  2  3
D56V9, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0                4                 24
  R1                3                  2
  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
  16Q LOSS MUTATED       1                         0     6
  16Q LOSS WILD-TYPE     2                         2    25
D56V10, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    6                 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(57) Variable = 17P LOSS MUTATION ANALYSIS
D57V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    7  3
  17P LOSS WILD-TYPE 11 15
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                10                 26 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 15 
$`17P LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2O 
       11.15        13.22        23.31        10.16        20.02        21.04 
TCGA-W5-AA2R TCGA-W5-AA38 TCGA-W6-AA0S TCGA-ZH-A8Y4 
       48.82        31.69        18.05        24.36 

$`17P LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q 
       14.63         6.77        64.96        20.88        63.75         1.64 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-WD-A7RX 
        0.33        35.18        18.25        46.09         5.59         0.69 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85         5.56        12.66        23.05        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.16               0.33 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             48.82              64.96 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            20.530             15.845 
[1] "10.2 - 48.8 (20.5)" "0.3 - 65.0 (15.8)" 
[1] "hr=" "2.1"
D57V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  17P LOSS MUTATED         7        2         0        0         0         1
  17P LOSS WILD-TYPE      12        7         1        2         2         2
D57V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  7                 12
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  17P LOSS MUTATED    7  2  1
  17P LOSS WILD-TYPE 12 10  4
D57V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                7                 12
  T2                2                 10
  T3                1                  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"
D57V5, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    9  1
  17P LOSS WILD-TYPE 17  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      9    1
  17P LOSS WILD-TYPE   17    4
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                9                 17
  1                1                  4
[1] 2 2
[1] FALSE
D57V6, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    8  1
  17P LOSS WILD-TYPE 20  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8    1
  17P LOSS WILD-TYPE   20    4
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0                8                 20
  1                1                  4
[1] 2 2
[1] FALSE
D57V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED    6  4
  17P LOSS WILD-TYPE 14 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      6    4
  17P LOSS WILD-TYPE   14   12
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                6                 14
  MALE                  4                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  17P LOSS MUTATED                            1
  17P LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  17P LOSS MUTATED                                     1
  17P LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  17P LOSS MUTATED                                  8
  17P LOSS WILD-TYPE                               22
D57V8, multiclass
                                     clus
vv                                    17P LOSS MUTATED 17P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  17P LOSS MUTATED    8  2  0
  17P LOSS WILD-TYPE 20  3  3
D57V9, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0                8                 20
  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
  17P LOSS MUTATED       2                         0     8
  17P LOSS WILD-TYPE     1                         2    23
D57V10, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    8                 23
[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(58) Variable = 18P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  3
  18P LOSS WILD-TYPE 15 15
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 6                 30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 15 
$`18P LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-W5-AA2G TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 
       11.15        14.63        10.16        64.96        24.36        33.37 

$`18P LOSS WILD-TYPE`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I 
       13.22        23.31        20.02         6.77        20.88        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W 
       21.04         1.64        48.82        40.11        20.61        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
        8.91         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
        5.56        12.66        23.05        17.06        13.45         3.22 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             10.16               0.33 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             64.96              63.75 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            19.495             18.150 
[1] "10.2 - 65.0 (19.5)" "0.3 - 63.8 (18.1)" 
[1] "hr=" "1.4"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  18P LOSS MUTATED         3        2         0        0         0         1
  18P LOSS WILD-TYPE      16        7         1        2         2         2
D58V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 2                  7
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  18P LOSS MUTATED    3  2  1
  18P LOSS WILD-TYPE 16 10  4
D58V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                3                 16
  T2                2                 10
  T3                1                  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"
D58V5, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    4  1
  18P LOSS WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      4    1
  18P LOSS WILD-TYPE   22    4
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                4                 22
  1                1                  4
[1] 2 2
[1] FALSE
D58V6, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    5  1
  18P LOSS WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5    1
  18P LOSS WILD-TYPE   23    4
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0                5                 23
  1                1                  4
[1] 2 2
[1] FALSE
D58V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED    2  4
  18P LOSS WILD-TYPE 18 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    4
  18P LOSS WILD-TYPE   18   12
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                2                 18
  MALE                  4                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  18P LOSS MUTATED                            0
  18P LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  18P LOSS MUTATED                                     0
  18P LOSS WILD-TYPE                                   4
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  18P LOSS MUTATED                                  6
  18P LOSS WILD-TYPE                               24
D58V8, multiclass
                                     clus
vv                                    18P LOSS MUTATED 18P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                0                  4
  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
  18P LOSS MUTATED    5  1  0
  18P LOSS WILD-TYPE 23  4  3
D58V9, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                5                 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
  18P LOSS MUTATED       2                         0     4
  18P LOSS WILD-TYPE     1                         2    27
D58V10, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                 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(59) Variable = 18Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  3
  18Q LOSS WILD-TYPE 13 15
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 8                 28 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 3                 15 
$`18Q LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2G 
       11.15        14.63        13.22        23.31        10.16        64.96 
TCGA-W5-AA2Q TCGA-ZH-A8Y4 
        1.64        24.36 

$`18Q LOSS WILD-TYPE`
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R 
       20.02         6.77        20.88        63.75        21.04        48.82 
TCGA-W5-AA2T TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       40.11        20.61        30.38         8.91         5.10        35.47 
TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        0.33        35.18        18.25        46.09        31.69         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 
       18.05         0.69         0.85         5.56        12.66        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       33.37        17.06        13.45         3.22 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              1.64               0.33 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             64.96              63.75 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            13.925             19.135 
[1] "1.6 - 65.0 (13.9)" "0.3 - 63.8 (19.1)"
[1] "hr=" "1.5"
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  18Q LOSS MUTATED         4        3         0        0         0         1
  18Q LOSS WILD-TYPE      15        6         1        2         2         2
D59V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  4                 15
  STAGE II                 3                  6
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  18Q LOSS MUTATED    4  3  1
  18Q LOSS WILD-TYPE 15  9  4
D59V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                4                 15
  T2                3                  9
  T3                1                  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"
D59V5, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    6  1
  18Q LOSS WILD-TYPE 20  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      6    1
  18Q LOSS WILD-TYPE   20    4
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                6                 20
  1                1                  4
[1] 2 2
[1] FALSE
D59V6, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    7  1
  18Q LOSS WILD-TYPE 21  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      7    1
  18Q LOSS WILD-TYPE   21    4
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0                7                 21
  1                1                  4
[1] 2 2
[1] FALSE
D59V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED    4  4
  18Q LOSS WILD-TYPE 16 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    4
  18Q LOSS WILD-TYPE   16   12
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                4                 16
  MALE                  4                 12
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  18Q LOSS MUTATED                            1
  18Q LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  18Q LOSS MUTATED                                     1
  18Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  18Q LOSS MUTATED                                  6
  18Q LOSS WILD-TYPE                               24
D59V8, multiclass
                                     clus
vv                                    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  18Q LOSS MUTATED    7  1  0
  18Q LOSS WILD-TYPE 21  4  3
D59V9, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                7                 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
  18Q LOSS MUTATED       2                         0     6
  18Q LOSS WILD-TYPE     1                         2    25
D59V10, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    6                 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(60) Variable = 19P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    2  2
  19P LOSS WILD-TYPE 16 16
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 32 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 16 
$`19P LOSS MUTATED`
TCGA-3X-AAVC TCGA-W5-AA2G TCGA-W5-AA2O TCGA-W5-AA2X 
       23.31        64.96        21.04         8.91 

$`19P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        10.16        20.02         6.77 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        63.75         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 TCGA-W5-AA34 
       30.38         5.10        35.47         0.33        35.18        18.25 
TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       46.09        31.69         5.59        18.05         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        5.56        12.66        23.05        24.36        33.37        17.06 
TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       13.45         3.22 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              8.91               0.33 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             64.96              63.75 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            22.175             17.555 
[1] "8.9 - 65.0 (22.2)" "0.3 - 63.8 (17.6)"
[1] "hr=" "1.7"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  19P LOSS MUTATED         3        0         0        0         0         1
  19P LOSS WILD-TYPE      16        9         1        2         2         2
D60V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  19P LOSS MUTATED    3  1  0
  19P LOSS WILD-TYPE 16 11  5
D60V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V5, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  1
  19P LOSS WILD-TYPE 23  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    1
  19P LOSS WILD-TYPE   23    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                3                 23
  1                1                  4
[1] 2 2
[1] FALSE
D60V6, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    3  1
  19P LOSS WILD-TYPE 25  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      3    1
  19P LOSS WILD-TYPE   25    4
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0                3                 25
  1                1                  4
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    2  2
  19P LOSS WILD-TYPE 18 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      2    2
  19P LOSS WILD-TYPE   18   14
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                2                 18
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  19P LOSS MUTATED                            0
  19P LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  19P LOSS MUTATED                                     2
  19P LOSS WILD-TYPE                                   2
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  19P LOSS MUTATED                                  2
  19P LOSS WILD-TYPE                               28
D60V8, multiclass
                                     clus
vv                                    19P LOSS MUTATED 19P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                2                  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
  19P LOSS MUTATED    3  0  1
  19P LOSS WILD-TYPE 25  5  2
D60V9, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                3                 25
  R1                0                  5
  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
  19P LOSS MUTATED       0                         0     4
  19P LOSS WILD-TYPE     3                         2    27
D60V10, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                 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(61) Variable = 19Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 17 16
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 33 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 2                 16 
$`19Q LOSS MUTATED`
TCGA-3X-AAVC TCGA-W5-AA2O TCGA-ZU-A8S4 
       23.31        21.04         3.22 

$`19Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        14.63        13.22        10.16        20.02         6.77 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T 
       64.96        20.88        63.75         1.64        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 
       20.61        30.38         8.91         5.10        35.47         0.33 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       35.18        18.25        46.09        31.69         5.59        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y4 
        0.69         0.85         5.56        12.66        23.05        24.36 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
       33.37        17.06        13.45 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              3.22               0.33 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             23.31              64.96 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             21.04              18.05 
[1] "3.2 - 23.3 (21.0)" "0.3 - 65.0 (18.1)"
[1] "hr=" "1.8"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  19Q LOSS MUTATED         3        0         0        0         0         0
  19Q LOSS WILD-TYPE      16        9         1        2         2         3
D61V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  19Q LOSS MUTATED    3  0  0
  19Q LOSS WILD-TYPE 16 12  5
D61V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                3                 16
  T2                0                 12
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V5, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  0
  19Q LOSS WILD-TYPE 24  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    0
  19Q LOSS WILD-TYPE   24    5
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 24
  1                0                  5
[1] 2 2
[1] FALSE
D61V6, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    2  0
  19Q LOSS WILD-TYPE 26  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      2    0
  19Q LOSS WILD-TYPE   26    5
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                2                 26
  1                0                  5
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED    1  2
  19Q LOSS WILD-TYPE 19 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1    2
  19Q LOSS WILD-TYPE   19   14
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                1                 19
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  19Q LOSS MUTATED                            0
  19Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  19Q LOSS MUTATED                                     1
  19Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  19Q LOSS MUTATED                                  2
  19Q LOSS WILD-TYPE                               28
D61V8, multiclass
                                     clus
vv                                    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  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
  19Q LOSS MUTATED    3  0  0
  19Q LOSS WILD-TYPE 25  5  3
D61V9, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0                3                 25
  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
  19Q LOSS MUTATED       0                         0     3
  19Q LOSS WILD-TYPE     3                         2    28
D61V10, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    3                 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(62) Variable = 20P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    4  1
  20P LOSS WILD-TYPE 14 17
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 31 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 17 
$`20P LOSS MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W6-AA0S TCGA-ZH-A8Y4 
       13.22        23.31        10.16        18.05        24.36 

$`20P LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H 
       11.15        14.63        20.02         6.77        64.96        20.88 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2U 
       63.75        21.04         1.64        48.82        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       30.38         8.91         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
       18.25        46.09        31.69         5.59         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        5.56        12.66        23.05        33.37        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             10.16               0.33 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             24.36              64.96 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             18.05              18.25 
[1] "10.2 - 24.4 (18.1)" "0.3 - 65.0 (18.2)" 
[1] "hr=" "2.3"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  20P LOSS MUTATED         3        1         0        0         0         1
  20P LOSS WILD-TYPE      16        8         1        2         2         2
D62V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                 16
  STAGE II                 1                  8
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  20P LOSS MUTATED    3  1  1
  20P LOSS WILD-TYPE 16 11  4
D62V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                 16
  T2                1                 11
  T3                1                  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"
D62V5, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    4  1
  20P LOSS WILD-TYPE 22  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    1
  20P LOSS WILD-TYPE   22    4
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                4                 22
  1                1                  4
[1] 2 2
[1] FALSE
D62V6, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  1
  20P LOSS WILD-TYPE 25  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    1
  20P LOSS WILD-TYPE   25    4
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                3                 25
  1                1                  4
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED    3  2
  20P LOSS WILD-TYPE 17 14
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      3    2
  20P LOSS WILD-TYPE   17   14
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                3                 17
  MALE                  2                 14
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  20P LOSS MUTATED                            1
  20P LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  20P LOSS MUTATED                                     1
  20P LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  20P LOSS MUTATED                                  3
  20P LOSS WILD-TYPE                               27
D62V8, multiclass
                                     clus
vv                                    20P LOSS MUTATED 20P LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  20P LOSS MUTATED    4  1  0
  20P LOSS WILD-TYPE 24  4  3
D62V9, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0                4                 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
  20P LOSS MUTATED       1                         0     4
  20P LOSS WILD-TYPE     2                         2    27
D62V10, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    1                  2
  BLACK OR AFRICAN AMERICAN                0                  2
  WHITE                                    4                 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(63) Variable = 21Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    8  7
  21Q LOSS WILD-TYPE 10 11
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                15                 21 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 7                 11 
$`21Q LOSS MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2U 
       11.15        13.22        23.31        10.16        20.02        20.61 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-ZH-A8Y2 
        5.10        35.47        18.25         5.59        18.05        23.05 
TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       24.36        13.45         3.22 

$`21Q LOSS WILD-TYPE`
TCGA-3X-AAVA TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O 
       14.63         6.77        64.96        20.88        63.75        21.04 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2T TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA31 
        1.64        48.82        40.11        30.38         8.91         0.33 
TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 
       35.18        46.09        31.69         0.69         0.85         5.56 
TCGA-ZH-A8Y1 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       12.66        33.37        17.06 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              3.22               0.33 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             35.47              64.96 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             18.05              20.88 
[1] "3.2 - 35.5 (18.1)" "0.3 - 65.0 (20.9)"
[1] "hr=" "1.6"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  21Q LOSS MUTATED        10        4         0        0         0         1
  21Q LOSS WILD-TYPE       9        5         1        2         2         2
D63V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 10                  9
  STAGE II                 4                  5
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  21Q LOSS MUTATED   10  4  1
  21Q LOSS WILD-TYPE  9  8  4
D63V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               10                  9
  T2                4                  8
  T3                1                  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"
D63V5, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12  1
  21Q LOSS WILD-TYPE 14  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12    1
  21Q LOSS WILD-TYPE   14    4
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               12                 14
  1                1                  4
[1] 2 2
[1] FALSE
D63V6, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   12  1
  21Q LOSS WILD-TYPE 16  4
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     12    1
  21Q LOSS WILD-TYPE   16    4
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               12                 16
  1                1                  4
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    8  7
  21Q LOSS WILD-TYPE 12  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      8    7
  21Q LOSS WILD-TYPE   12    9
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                8                 12
  MALE                  7                  9
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  21Q LOSS MUTATED                            1
  21Q LOSS WILD-TYPE                          1
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  21Q LOSS MUTATED                                     1
  21Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  21Q LOSS MUTATED                                 13
  21Q LOSS WILD-TYPE                               17
D63V8, multiclass
                                     clus
vv                                    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         1                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                  13                 17
[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
  21Q LOSS MUTATED   11  3  1
  21Q LOSS WILD-TYPE 17  2  2
D63V9, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               11                 17
  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
  21Q LOSS MUTATED       2                         1    12
  21Q LOSS WILD-TYPE     1                         1    19
D63V10, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    2                  1
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                   12                 19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 22Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    4  1
  22Q LOSS WILD-TYPE 14 17
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                 31 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                 17 
$`22Q LOSS MUTATED`
TCGA-3X-AAVC TCGA-4G-AAZT TCGA-W5-AA2R TCGA-W6-AA0S TCGA-ZH-A8Y2 
       23.31         6.77        48.82        18.05        23.05 

$`22Q LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVA TCGA-3X-AAVB TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       11.15        14.63        13.22        10.16        20.02        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2T TCGA-W5-AA2U 
       20.88        63.75        21.04         1.64        40.11        20.61 
TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA31 TCGA-W5-AA33 
       30.38         8.91         5.10        35.47         0.33        35.18 
TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A 
       18.25        46.09        31.69         5.59         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 
        5.56        12.66        24.36        33.37        17.06        13.45 
TCGA-ZU-A8S4 
        3.22 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              6.77               0.33 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             48.82              64.96 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             23.05              17.06 
[1] "6.8 - 48.8 (23.1)" "0.3 - 65.0 (17.1)"
[1] "hr=" "3.3"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  22Q LOSS MUTATED         5        0         0        0         0         0
  22Q LOSS WILD-TYPE      14        9         1        2         2         3
D64V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                  5                 14
  STAGE II                 0                  9
  STAGE III                0                  1
  STAGE IV                 0                  2
  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
  22Q LOSS MUTATED    5  0  0
  22Q LOSS WILD-TYPE 14 12  5
D64V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                5                 14
  T2                0                 12
  T3                0                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V5, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  0
  22Q LOSS WILD-TYPE 22  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    0
  22Q LOSS WILD-TYPE   22    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                4                 22
  1                0                  5
[1] 2 2
[1] FALSE
D64V6, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  0
  22Q LOSS WILD-TYPE 24  5
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    0
  22Q LOSS WILD-TYPE   24    5
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0                4                 24
  1                0                  5
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED    4  1
  22Q LOSS WILD-TYPE 16 15
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      4    1
  22Q LOSS WILD-TYPE   16   15
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                4                 16
  MALE                  1                 15
[1] 2 2
[1] FALSE
                    vv
clus                 CHOLANGIOCARCINOMA; DISTAL
  22Q LOSS MUTATED                            0
  22Q LOSS WILD-TYPE                          2
                    vv
clus                 CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  22Q LOSS MUTATED                                     1
  22Q LOSS WILD-TYPE                                   3
                    vv
clus                 CHOLANGIOCARCINOMA; INTRAHEPATIC
  22Q LOSS MUTATED                                  4
  22Q LOSS WILD-TYPE                               26
D64V8, multiclass
                                     clus
vv                                    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                         0                  2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                1                  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
  22Q LOSS MUTATED    5  0  0
  22Q LOSS WILD-TYPE 23  5  3
D64V9, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0                5                 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
  22Q LOSS MUTATED       0                         1     4
  22Q LOSS WILD-TYPE     3                         1    27
D64V10, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  3
  BLACK OR AFRICAN AMERICAN                1                  1
  WHITE                                    4                 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(65) Variable = XP LOSS MUTATION ANALYSIS
D65V1, survival
                   sevent
clus2                0  1
  XP LOSS MUTATED    5 10
  XP LOSS WILD-TYPE 13  8
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               15                21 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               10                 8 
$`XP LOSS MUTATED`
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
       14.63        20.02        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S 
       20.61        35.47        18.25        46.09        31.69        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y4 
        0.69         0.85        24.36 

$`XP LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        13.22        23.31        10.16         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 
       20.88         1.64        30.38         8.91         5.10         0.33 
TCGA-W5-AA33 TCGA-W5-AA39 TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       35.18         5.59         5.56        12.66        23.05        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.69              0.33 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            63.75             64.96 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            21.04             12.66 
[1] "0.7 - 63.8 (21.0)" "0.3 - 65.0 (12.7)"
[1] "hr=" "1"  
D65V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  XP LOSS MUTATED         9        4         0        2         0         0
  XP LOSS WILD-TYPE      10        5         1        0         2         3
D65V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                 9                10
  STAGE II                4                 5
  STAGE III               0                 1
  STAGE IV                2                 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
  XP LOSS MUTATED    9  5  1
  XP LOSS WILD-TYPE 10  7  4
D65V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1               9                10
  T2               5                 7
  T3               1                 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"
D65V5, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   12  0
  XP LOSS WILD-TYPE 14  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     12    0
  XP LOSS WILD-TYPE   14    5
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              12                14
  1               0                 5
[1] 2 2
[1] FALSE
D65V6, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   11  2
  XP LOSS WILD-TYPE 17  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     11    2
  XP LOSS WILD-TYPE   17    3
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              11                17
  1               2                 3
[1] 2 2
[1] FALSE
D65V7, binary
                   cls
clus                 0  1
  XP LOSS MUTATED   10  5
  XP LOSS WILD-TYPE 10 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     10    5
  XP LOSS WILD-TYPE   10   11
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              10                10
  MALE                 5                11
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  XP LOSS MUTATED                            0
  XP LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  XP LOSS MUTATED                                     2
  XP LOSS WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  XP LOSS MUTATED                                 13
  XP LOSS WILD-TYPE                               17
D65V8, multiclass
                                     clus
vv                                    XP LOSS MUTATED XP LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 13                17
[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
  XP LOSS MUTATED   11  3  1
  XP LOSS WILD-TYPE 17  2  2
D65V9, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  R0              11                17
  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
  XP LOSS MUTATED       0                         0    15
  XP LOSS WILD-TYPE     3                         2    16
D65V10, multiclass
                           clus
vv                          XP LOSS MUTATED XP LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  15                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = XQ LOSS MUTATION ANALYSIS
D66V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED    5 10
  XQ LOSS WILD-TYPE 13  8
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               15                21 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               10                 8 
$`XQ LOSS MUTATED`
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2T 
       14.63        20.02        63.75        21.04        48.82        40.11 
TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S 
       20.61        35.47        18.25        46.09        31.69        18.05 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y4 
        0.69         0.85        24.36 

$`XQ LOSS WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2G 
       11.15        13.22        23.31        10.16         6.77        64.96 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA31 
       20.88         1.64        30.38         8.91         5.10         0.33 
TCGA-W5-AA33 TCGA-W5-AA39 TCGA-ZD-A8I3 TCGA-ZH-A8Y1 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       35.18         5.59         5.56        12.66        23.05        33.37 
TCGA-ZH-A8Y6 TCGA-ZH-A8Y8 TCGA-ZU-A8S4 
       17.06        13.45         3.22 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.69              0.33 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            63.75             64.96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            21.04             12.66 
[1] "0.7 - 63.8 (21.0)" "0.3 - 65.0 (12.7)"
[1] "hr=" "1"  
D66V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV STAGE IVA STAGE IVB
  XQ LOSS MUTATED         9        4         0        2         0         0
  XQ LOSS WILD-TYPE      10        5         1        0         2         3
D66V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                 9                10
  STAGE II                4                 5
  STAGE III               0                 1
  STAGE IV                2                 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
  XQ LOSS MUTATED    9  5  1
  XQ LOSS WILD-TYPE 10  7  4
D66V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               9                10
  T2               5                 7
  T3               1                 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"
D66V5, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   12  0
  XQ LOSS WILD-TYPE 14  5
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     12    0
  XQ LOSS WILD-TYPE   14    5
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              12                14
  1               0                 5
[1] 2 2
[1] FALSE
D66V6, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   11  2
  XQ LOSS WILD-TYPE 17  3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     11    2
  XQ LOSS WILD-TYPE   17    3
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              11                17
  1               2                 3
[1] 2 2
[1] FALSE
D66V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   10  5
  XQ LOSS WILD-TYPE 10 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     10    5
  XQ LOSS WILD-TYPE   10   11
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              10                10
  MALE                 5                11
[1] 2 2
[1] FALSE
                   vv
clus                CHOLANGIOCARCINOMA; DISTAL
  XQ LOSS MUTATED                            0
  XQ LOSS WILD-TYPE                          2
                   vv
clus                CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  XQ LOSS MUTATED                                     2
  XQ LOSS WILD-TYPE                                   2
                   vv
clus                CHOLANGIOCARCINOMA; INTRAHEPATIC
  XQ LOSS MUTATED                                 13
  XQ LOSS WILD-TYPE                               17
D66V8, multiclass
                                     clus
vv                                    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                        0                 2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR               2                 2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                 13                17
[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
  XQ LOSS MUTATED   11  3  1
  XQ LOSS WILD-TYPE 17  2  2
D66V9, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              11                17
  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
  XQ LOSS MUTATED       0                         0    15
  XQ LOSS WILD-TYPE     3                         2    16
D66V10, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   0                 3
  BLACK OR AFRICAN AMERICAN               0                 2
  WHITE                                  15                16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
