[1] "ofn"        "-oTCHOL-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/CHOL-TP/22489349/CHOL-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/CHOL-TP/22519029/transformed.cor.cli.txt"

nPatients in clinical file=45, in cluster file=36, common to both=36
[1] 20 36
[1] "AMP PEAK 1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                        24                         12 
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                        24                         12 
[1] "AMP PEAK 2(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                            8                            28 
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                            8                            28 
[1] "AMP PEAK 3(12Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                           10                            26 
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                           10                            26 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            30                              6 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            30                              6 
[1] "DEL PEAK  2(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                           28                             8 
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                           28                             8 
[1] "DEL PEAK  3(3P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                         28                           8 
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                         28                           8 
[1] "DEL PEAK  4(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           23                            13 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           23                            13 
[1] "DEL PEAK  5(5Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                            8                            28 
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                            8                            28 
[1] "DEL PEAK  6(6Q13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                         21                          15 
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                         21                          15 
[1] "DEL PEAK  7(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           23                            13 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           23                            13 
[1] "DEL PEAK  8(9Q21.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                            19                             17 
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                            19                             17 
[1] "DEL PEAK  9(10Q26.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                             12                              24 
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                             12                              24 
[1] "DEL PEAK 10(11Q25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                          13                           23 
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                          13                           23 
[1] "DEL PEAK 11(12Q24.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                              8                              28 
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                              8                              28 
[1] "DEL PEAK 12(13Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                             16                              20 
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                             16                              20 
[1] "DEL PEAK 13(14Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                            14                             22 
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                            14                             22 
[1] "DEL PEAK 14(14Q32.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                             20                              16 
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                             20                              16 
[1] "DEL PEAK 15(14Q32.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                             20                              16 
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                             20                              16 
[1] "DEL PEAK 16(14Q32.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                             20                              16 
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                             20                              16 
[1] "DEL PEAK 17(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             7                             29 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             7                             29 
[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=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "2"                "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 = AMP PEAK 1(1Q22) MUTATION ANALYSIS
D1V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 1(1Q22) MUTATED   11 13
  AMP PEAK 1(1Q22) WILD-TYPE  7  5
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                        24                         12 
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                        13                          5 
$`AMP PEAK 1(1Q22) MUTATED`
TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       40.11         0.33        12.66        24.36        19.79        14.63 
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W 
       21.37        38.70        13.81         1.64        50.70        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 
        8.91        53.06        37.91        47.64        18.25        46.09 
TCGA-W5-AA39 TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
        5.59         0.69         0.85         5.56        23.05        40.41 

$`AMP PEAK 1(1Q22) 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        35.41        63.75 
TCGA-W5-AA2O TCGA-W5-AA2U TCGA-W5-AA38 TCGA-W6-AA0S TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       21.04        20.61        48.36        26.56        17.06         3.22 

  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                      0.33                       3.22 
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                     53.06                      64.96 
  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE 
                    20.580                     22.175 
[1] "0.3 - 53.1 (20.6)" "3.2 - 65.0 (22.2)"
[1] "hr=" "1.9"
D1V2, continuous
                            vv
clus                         STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 1(1Q22) MUTATED         9        9         0        2         2
  AMP PEAK 1(1Q22) WILD-TYPE      10        0         1        0         0
                            vv
clus                         STAGE IVB
  AMP PEAK 1(1Q22) MUTATED           2
  AMP PEAK 1(1Q22) WILD-TYPE         1
D1V3, multiclass
           clus
vv          AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  STAGE I                          9                         10
  STAGE II                         9                          0
  STAGE III                        0                          1
  STAGE IV                         2                          0
  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
  AMP PEAK 1(1Q22) MUTATED    9 12  3
  AMP PEAK 1(1Q22) WILD-TYPE 10  0  2
D1V4, multiclass
    clus
vv   AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  T1                        9                         10
  T2                       12                          0
  T3                        3                          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"
D1V5, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q22) MUTATED   16  4
  AMP PEAK 1(1Q22) WILD-TYPE 10  1
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q22) MUTATED     16    4
  AMP PEAK 1(1Q22) WILD-TYPE   10    1
   clus
vv  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  0                       16                         10
  1                        4                          1
[1] 2 2
[1] FALSE
D1V6, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q22) MUTATED   19  4
  AMP PEAK 1(1Q22) WILD-TYPE  9  1
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q22) MUTATED     19    4
  AMP PEAK 1(1Q22) WILD-TYPE    9    1
   clus
vv  AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  0                       19                          9
  1                        4                          1
[1] 2 2
[1] FALSE
D1V7, binary
                            cls
clus                          0  1
  AMP PEAK 1(1Q22) MUTATED   12 12
  AMP PEAK 1(1Q22) WILD-TYPE  8  4
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 1(1Q22) MUTATED     12   12
  AMP PEAK 1(1Q22) WILD-TYPE    8    4
        clus
vv       AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  FEMALE                       12                          8
  MALE                         12                          4
[1] 2 2
[1] FALSE
                            vv
clus                         CHOLANGIOCARCINOMA; DISTAL
  AMP PEAK 1(1Q22) MUTATED                            0
  AMP PEAK 1(1Q22) WILD-TYPE                          2
                            vv
clus                         CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  AMP PEAK 1(1Q22) MUTATED                                     3
  AMP PEAK 1(1Q22) WILD-TYPE                                   1
                            vv
clus                         CHOLANGIOCARCINOMA; INTRAHEPATIC
  AMP PEAK 1(1Q22) MUTATED                                 21
  AMP PEAK 1(1Q22) WILD-TYPE                                9
D1V8, multiclass
                                     clus
vv                                    AMP PEAK 1(1Q22) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                 0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                        3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                          21
                                     clus
vv                                    AMP PEAK 1(1Q22) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                   2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                          1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                             9
[1] 3 2
[1] 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
  AMP PEAK 1(1Q22) MUTATED   16  5  3
  AMP PEAK 1(1Q22) WILD-TYPE 12  0  0
D1V9, multiclass
    clus
vv   AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  R0                       16                         12
  R1                        5                          0
  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
  AMP PEAK 1(1Q22) MUTATED       2                         1    21
  AMP PEAK 1(1Q22) WILD-TYPE     1                         1    10
D1V10, multiclass
                           clus
vv                          AMP PEAK 1(1Q22) MUTATED AMP PEAK 1(1Q22) WILD-TYPE
  ASIAN                                            2                          1
  BLACK OR AFRICAN AMERICAN                        1                          1
  WHITE                                           21                         10
[1] 3 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 = AMP PEAK 2(11Q13.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 2(11Q13.3) MUTATED    2  6
  AMP PEAK 2(11Q13.3) WILD-TYPE 16 12
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                            8                            28 
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                            6                            12 
$`AMP PEAK 2(11Q13.3) MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA2X TCGA-W5-AA30 TCGA-WD-A7RX 
       11.15        13.22        40.11         8.91        37.91         0.69 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        5.56        23.05 

$`AMP PEAK 2(11Q13.3) WILD-TYPE`
TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC 
        0.33        12.66        24.36        19.79        14.63        23.31 
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I 
       21.37        38.70        13.81        64.96        35.41        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z 
       21.04         1.64        50.70        20.61        30.38        53.06 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       47.64        18.25        46.09        48.36         5.59        26.56 
TCGA-YR-A95A TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.85        40.41        17.06         3.22 

  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                         0.69                          0.33 
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                        40.11                         64.96 
  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE 
                       12.185                        22.340 
[1] "0.7 - 40.1 (12.2)" "0.3 - 65.0 (22.3)"
[1] "hr=" "2.9"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 2(11Q13.3) MUTATED         3        3         0        0         0
  AMP PEAK 2(11Q13.3) WILD-TYPE      16        6         1        2         2
                               vv
clus                            STAGE IVB
  AMP PEAK 2(11Q13.3) MUTATED           2
  AMP PEAK 2(11Q13.3) WILD-TYPE         1
D2V3, multiclass
           clus
vv          AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE
  STAGE I                             3                            16
  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
  AMP PEAK 2(11Q13.3) MUTATED    3  4  1
  AMP PEAK 2(11Q13.3) WILD-TYPE 16  8  4
D2V4, multiclass
    clus
vv   AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE
  T1                           3                            16
  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"
D2V5, binary
                               cls
clus                             0  1
  AMP PEAK 2(11Q13.3) MUTATED    4  2
  AMP PEAK 2(11Q13.3) WILD-TYPE 22  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(11Q13.3) MUTATED      4    2
  AMP PEAK 2(11Q13.3) WILD-TYPE   22    3
   clus
vv  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE
  0                           4                            22
  1                           2                             3
[1] 2 2
[1] FALSE
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK 2(11Q13.3) MUTATED    5  2
  AMP PEAK 2(11Q13.3) WILD-TYPE 23  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(11Q13.3) MUTATED      5    2
  AMP PEAK 2(11Q13.3) WILD-TYPE   23    3
   clus
vv  AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE
  0                           5                            23
  1                           2                             3
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK 2(11Q13.3) MUTATED    5  3
  AMP PEAK 2(11Q13.3) WILD-TYPE 15 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 2(11Q13.3) MUTATED      5    3
  AMP PEAK 2(11Q13.3) WILD-TYPE   15   13
        clus
vv       AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) WILD-TYPE
  FEMALE                           5                            15
  MALE                             3                            13
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  AMP PEAK 2(11Q13.3) MUTATED                            1
  AMP PEAK 2(11Q13.3) WILD-TYPE                          1
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  AMP PEAK 2(11Q13.3) MUTATED                                     1
  AMP PEAK 2(11Q13.3) WILD-TYPE                                   3
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  AMP PEAK 2(11Q13.3) MUTATED                                  6
  AMP PEAK 2(11Q13.3) WILD-TYPE                               24
D2V8, multiclass
                                     clus
vv                                    AMP PEAK 2(11Q13.3) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              6
                                     clus
vv                                    AMP PEAK 2(11Q13.3) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               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
  AMP PEAK 2(11Q13.3) MUTATED    6  0  2
  AMP PEAK 2(11Q13.3) WILD-TYPE 22  5  1
D2V9, multiclass
    clus
vv   AMP PEAK 2(11Q13.3) MUTATED AMP PEAK 2(11Q13.3) 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
  AMP PEAK 2(11Q13.3) MUTATED       2                         1     5
  AMP PEAK 2(11Q13.3) WILD-TYPE     1                         1    26
D2V10, multiclass
                           clus
vv                          AMP PEAK 2(11Q13.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               5
                           clus
vv                          AMP PEAK 2(11Q13.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK 3(12Q13.2) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 3(12Q13.2) MUTATED    4  6
  AMP PEAK 3(12Q13.2) WILD-TYPE 14 12
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                           10                            26 
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                            6                            12 
$`AMP PEAK 3(12Q13.2) MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2X 
       11.15         0.33        24.36        21.37        13.81         8.91 
TCGA-W5-AA2Z TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       53.06        18.25         5.56        23.05 

$`AMP PEAK 3(12Q13.2) WILD-TYPE`
TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVC 
       13.22        40.11        12.66        19.79        14.63        23.31 
TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q 
       38.70        64.96        35.41        63.75        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA36 
       50.70        20.61        30.38        37.91        47.64        46.09 
TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y5 
       48.36         5.59        26.56         0.69         0.85        40.41 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                         0.33                          0.69 
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                        53.06                         64.96 
  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE 
                       16.030                        24.935 
[1] "0.3 - 53.1 (16.0)" "0.7 - 65.0 (24.9)"
[1] "hr=" "2.1"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  AMP PEAK 3(12Q13.2) MUTATED         6        3         0        0         0
  AMP PEAK 3(12Q13.2) WILD-TYPE      13        6         1        2         2
                               vv
clus                            STAGE IVB
  AMP PEAK 3(12Q13.2) MUTATED           1
  AMP PEAK 3(12Q13.2) WILD-TYPE         2
D3V3, multiclass
           clus
vv          AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  STAGE I                             6                            13
  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
  AMP PEAK 3(12Q13.2) MUTATED    6  4  0
  AMP PEAK 3(12Q13.2) WILD-TYPE 13  8  5
D3V4, multiclass
    clus
vv   AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  T1                           6                            13
  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"
D3V5, binary
                               cls
clus                             0  1
  AMP PEAK 3(12Q13.2) MUTATED    8  1
  AMP PEAK 3(12Q13.2) WILD-TYPE 18  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12Q13.2) MUTATED      8    1
  AMP PEAK 3(12Q13.2) WILD-TYPE   18    4
   clus
vv  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  0                           8                            18
  1                           1                             4
[1] 2 2
[1] FALSE
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK 3(12Q13.2) MUTATED    9  1
  AMP PEAK 3(12Q13.2) WILD-TYPE 19  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12Q13.2) MUTATED      9    1
  AMP PEAK 3(12Q13.2) WILD-TYPE   19    4
   clus
vv  AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  0                           9                            19
  1                           1                             4
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK 3(12Q13.2) MUTATED    4  6
  AMP PEAK 3(12Q13.2) WILD-TYPE 16 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 3(12Q13.2) MUTATED      4    6
  AMP PEAK 3(12Q13.2) WILD-TYPE   16   10
        clus
vv       AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  FEMALE                           4                            16
  MALE                             6                            10
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  AMP PEAK 3(12Q13.2) MUTATED                            0
  AMP PEAK 3(12Q13.2) WILD-TYPE                          2
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  AMP PEAK 3(12Q13.2) MUTATED                                     1
  AMP PEAK 3(12Q13.2) WILD-TYPE                                   3
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  AMP PEAK 3(12Q13.2) MUTATED                                  9
  AMP PEAK 3(12Q13.2) WILD-TYPE                               21
D3V8, multiclass
                                     clus
vv                                    AMP PEAK 3(12Q13.2) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              9
                                     clus
vv                                    AMP PEAK 3(12Q13.2) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               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
  AMP PEAK 3(12Q13.2) MUTATED    7  2  1
  AMP PEAK 3(12Q13.2) WILD-TYPE 21  3  2
D3V9, multiclass
    clus
vv   AMP PEAK 3(12Q13.2) MUTATED AMP PEAK 3(12Q13.2) WILD-TYPE
  R0                           7                            21
  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
  AMP PEAK 3(12Q13.2) MUTATED       3                         1     6
  AMP PEAK 3(12Q13.2) WILD-TYPE     0                         1    25
D3V10, multiclass
                           clus
vv                          AMP PEAK 3(12Q13.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               6
                           clus
vv                          AMP PEAK 3(12Q13.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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(4) Variable = DEL PEAK  1(1P36.21) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.21) MUTATED   14 16
  DEL PEAK  1(1P36.21) WILD-TYPE  4  2
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            30                              6 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            16                              2 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       40.11         0.33        12.66        24.36        19.79        14.63 
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O 
       21.37        38.70        13.81        64.96        63.75        21.04 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z 
        1.64        50.70        20.61        30.38         8.91        53.06 
TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       37.91        47.64        18.25        46.09        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       26.56         0.69         0.85         5.56        23.05        40.41 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-3X-AAVC TCGA-W5-AA2H TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       11.15        13.22        23.31        35.41        17.06         3.22 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          0.33                           3.22 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                         64.96                          35.41 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                         22.21                          15.14 
[1] "0.3 - 65.0 (22.2)" "3.2 - 35.4 (15.1)"
[1] "hr=" "1"  
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  1(1P36.21) MUTATED        15        9         0        2         2
  DEL PEAK  1(1P36.21) WILD-TYPE       4        0         1        0         0
                                vv
clus                             STAGE IVB
  DEL PEAK  1(1P36.21) MUTATED           2
  DEL PEAK  1(1P36.21) WILD-TYPE         1
D4V3, multiclass
           clus
vv          DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  STAGE I                             15                              4
  STAGE II                             9                              0
  STAGE III                            0                              1
  STAGE IV                             2                              0
  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
  DEL PEAK  1(1P36.21) MUTATED   15 12  3
  DEL PEAK  1(1P36.21) WILD-TYPE  4  0  2
D4V4, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  T1                           15                              4
  T2                           12                              0
  T3                            3                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.21) MUTATED   22  4
  DEL PEAK  1(1P36.21) WILD-TYPE  4  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     22    4
  DEL PEAK  1(1P36.21) WILD-TYPE    4    1
   clus
vv  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  0                           22                              4
  1                            4                              1
[1] 2 2
[1] FALSE
D4V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.21) MUTATED   24  4
  DEL PEAK  1(1P36.21) WILD-TYPE  4  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     24    4
  DEL PEAK  1(1P36.21) WILD-TYPE    4    1
   clus
vv  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  0                           24                              4
  1                            4                              1
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.21) MUTATED   16 14
  DEL PEAK  1(1P36.21) WILD-TYPE  4  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.21) MUTATED     16   14
  DEL PEAK  1(1P36.21) WILD-TYPE    4    2
        clus
vv       DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  FEMALE                           16                              4
  MALE                             14                              2
[1] 2 2
[1] FALSE
                                vv
clus                             CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  1(1P36.21) MUTATED                            0
  DEL PEAK  1(1P36.21) WILD-TYPE                          2
                                vv
clus                             CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  1(1P36.21) MUTATED                                     3
  DEL PEAK  1(1P36.21) WILD-TYPE                                   1
                                vv
clus                             CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  1(1P36.21) MUTATED                                 27
  DEL PEAK  1(1P36.21) WILD-TYPE                                3
D4V8, multiclass
                                     clus
vv                                    DEL PEAK  1(1P36.21) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                     0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                            3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              27
                                     clus
vv                                    DEL PEAK  1(1P36.21) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                       2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                              1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             R0 R1 RX
  DEL PEAK  1(1P36.21) MUTATED   22  5  3
  DEL PEAK  1(1P36.21) WILD-TYPE  6  0  0
D4V9, multiclass
    clus
vv   DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE
  R0                           22                              6
  R1                            5                              0
  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
  DEL PEAK  1(1P36.21) MUTATED       2                         1    27
  DEL PEAK  1(1P36.21) WILD-TYPE     1                         1     4
D4V10, multiclass
                           clus
vv                          DEL PEAK  1(1P36.21) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               27
                           clus
vv                          DEL PEAK  1(1P36.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                  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"

Clustering(5) Variable = DEL PEAK  2(3P25.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(3P25.3) MUTATED   12 16
  DEL PEAK  2(3P25.3) WILD-TYPE  6  2
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                           28                             8 
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                           16                             2 
$`DEL PEAK  2(3P25.3) MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       11.15        40.11         0.33        24.36        19.79        14.63 
TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O 
       23.31        21.37        38.70        13.81        63.75        21.04 
TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 
       50.70        20.61        30.38         8.91        53.06        37.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       47.64        18.25        46.09        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
        0.69         0.85         5.56        23.05 

$`DEL PEAK  2(3P25.3) WILD-TYPE`
TCGA-3X-AAVB TCGA-ZH-A8Y1 TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-ZH-A8Y5 
       13.22        12.66        64.96        35.41         1.64        40.41 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                         0.33                          1.64 
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                        63.75                         64.96 
  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE 
                        22.21                         15.14 
[1] "0.3 - 63.8 (22.2)" "1.6 - 65.0 (15.1)"
[1] "hr=" "2.2"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  2(3P25.3) MUTATED        16        8         0        2         1
  DEL PEAK  2(3P25.3) WILD-TYPE       3        1         1        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK  2(3P25.3) MUTATED           1
  DEL PEAK  2(3P25.3) WILD-TYPE         2
D5V3, multiclass
           clus
vv          DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  STAGE I                            16                             3
  STAGE II                            8                             1
  STAGE III                           0                             1
  STAGE IV                            2                             0
  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
  DEL PEAK  2(3P25.3) MUTATED   16 11  1
  DEL PEAK  2(3P25.3) WILD-TYPE  3  1  4
D5V4, multiclass
    clus
vv   DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  T1                          16                             3
  T2                          11                             1
  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
  DEL PEAK  2(3P25.3) MUTATED   22  2
  DEL PEAK  2(3P25.3) WILD-TYPE  4  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P25.3) MUTATED     22    2
  DEL PEAK  2(3P25.3) WILD-TYPE    4    3
   clus
vv  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  0                          22                             4
  1                           2                             3
[1] 2 2
[1] FALSE
D5V6, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P25.3) MUTATED   23  3
  DEL PEAK  2(3P25.3) WILD-TYPE  5  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P25.3) MUTATED     23    3
  DEL PEAK  2(3P25.3) WILD-TYPE    5    2
   clus
vv  DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  0                          23                             5
  1                           3                             2
[1] 2 2
[1] FALSE
D5V7, binary
                               cls
clus                             0  1
  DEL PEAK  2(3P25.3) MUTATED   15 13
  DEL PEAK  2(3P25.3) WILD-TYPE  5  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(3P25.3) MUTATED     15   13
  DEL PEAK  2(3P25.3) WILD-TYPE    5    3
        clus
vv       DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  FEMALE                          15                             5
  MALE                            13                             3
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  2(3P25.3) MUTATED                            0
  DEL PEAK  2(3P25.3) WILD-TYPE                          2
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  2(3P25.3) MUTATED                                     4
  DEL PEAK  2(3P25.3) WILD-TYPE                                   0
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  2(3P25.3) MUTATED                                 24
  DEL PEAK  2(3P25.3) WILD-TYPE                                6
D5V8, multiclass
                                     clus
vv                                    DEL PEAK  2(3P25.3) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                             24
                                     clus
vv                                    DEL PEAK  2(3P25.3) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             0
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                6
[1] 3 2
[1] 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
  DEL PEAK  2(3P25.3) MUTATED   21  4  3
  DEL PEAK  2(3P25.3) WILD-TYPE  7  1  0
D5V9, multiclass
    clus
vv   DEL PEAK  2(3P25.3) MUTATED DEL PEAK  2(3P25.3) WILD-TYPE
  R0                          21                             7
  R1                           4                             1
  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
  DEL PEAK  2(3P25.3) MUTATED       3                         1    24
  DEL PEAK  2(3P25.3) WILD-TYPE     0                         1     7
D5V10, multiclass
                           clus
vv                          DEL PEAK  2(3P25.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              24
                           clus
vv                          DEL PEAK  2(3P25.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 7
[1] 3 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 = DEL PEAK  3(3P13) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(3P13) MUTATED   12 16
  DEL PEAK  3(3P13) WILD-TYPE  6  2
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                         28                           8 
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                         16                           2 
$`DEL PEAK  3(3P13) MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G 
       14.63        23.31        21.37        38.70        13.81        64.96 
TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X 
       63.75        21.04        50.70        20.61        30.38         8.91 
TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       53.06        37.91        18.25        46.09        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       26.56         0.69         5.56        23.05 

$`DEL PEAK  3(3P13) WILD-TYPE`
TCGA-3X-AAVB TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA33 TCGA-YR-A95A TCGA-ZH-A8Y5 
       13.22        35.41         1.64        47.64         0.85        40.41 
TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       17.06         3.22 

  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                       0.33                        0.85 
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                      64.96                       47.64 
  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE 
                      22.21                       15.14 
[1] "0.3 - 65.0 (22.2)" "0.8 - 47.6 (15.1)"
[1] "hr=" "1.7"
D6V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  3(3P13) MUTATED        16        8         0        1         2
  DEL PEAK  3(3P13) WILD-TYPE       3        1         1        1         0
                             vv
clus                          STAGE IVB
  DEL PEAK  3(3P13) MUTATED           1
  DEL PEAK  3(3P13) WILD-TYPE         2
D6V3, multiclass
           clus
vv          DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  STAGE I                          16                           3
  STAGE II                          8                           1
  STAGE III                         0                           1
  STAGE IV                          1                           1
  STAGE IVA                         2                           0
  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
  DEL PEAK  3(3P13) MUTATED   16 10  2
  DEL PEAK  3(3P13) WILD-TYPE  3  2  3
D6V4, multiclass
    clus
vv   DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  T1                        16                           3
  T2                        10                           2
  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"
D6V5, binary
                             cls
clus                           0  1
  DEL PEAK  3(3P13) MUTATED   22  3
  DEL PEAK  3(3P13) WILD-TYPE  4  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(3P13) MUTATED     22    3
  DEL PEAK  3(3P13) WILD-TYPE    4    2
   clus
vv  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  0                        22                           4
  1                         3                           2
[1] 2 2
[1] FALSE
D6V6, binary
                             cls
clus                           0  1
  DEL PEAK  3(3P13) MUTATED   24  2
  DEL PEAK  3(3P13) WILD-TYPE  4  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(3P13) MUTATED     24    2
  DEL PEAK  3(3P13) WILD-TYPE    4    3
   clus
vv  DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  0                        24                           4
  1                         2                           3
[1] 2 2
[1] FALSE
D6V7, binary
                             cls
clus                           0  1
  DEL PEAK  3(3P13) MUTATED   17 11
  DEL PEAK  3(3P13) WILD-TYPE  3  5
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(3P13) MUTATED     17   11
  DEL PEAK  3(3P13) WILD-TYPE    3    5
        clus
vv       DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  FEMALE                        17                           3
  MALE                          11                           5
[1] 2 2
[1] FALSE
                             vv
clus                          CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  3(3P13) MUTATED                            0
  DEL PEAK  3(3P13) WILD-TYPE                          2
                             vv
clus                          CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  3(3P13) MUTATED                                     3
  DEL PEAK  3(3P13) WILD-TYPE                                   1
                             vv
clus                          CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  3(3P13) MUTATED                                 25
  DEL PEAK  3(3P13) WILD-TYPE                                5
D6V8, multiclass
                                     clus
vv                                    DEL PEAK  3(3P13) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                  0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                         3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                           25
                                     clus
vv                                    DEL PEAK  3(3P13) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                    2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              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"
                             vv
clus                          R0 R1 RX
  DEL PEAK  3(3P13) MUTATED   21  4  3
  DEL PEAK  3(3P13) WILD-TYPE  7  1  0
D6V9, multiclass
    clus
vv   DEL PEAK  3(3P13) MUTATED DEL PEAK  3(3P13) WILD-TYPE
  R0                        21                           7
  R1                         4                           1
  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
  DEL PEAK  3(3P13) MUTATED       3                         1    24
  DEL PEAK  3(3P13) WILD-TYPE     0                         1     7
D6V10, multiclass
                           clus
vv                          DEL PEAK  3(3P13) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            24
                           clus
vv                          DEL PEAK  3(3P13) WILD-TYPE
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               7
[1] 3 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 = DEL PEAK  4(4Q34.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(4Q34.3) MUTATED   11 12
  DEL PEAK  4(4Q34.3) WILD-TYPE  7  6
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           23                            13 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                           12                             6 
$`DEL PEAK  4(4Q34.3) MUTATED`
TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVE TCGA-4G-AAZO 
       40.11         0.33        24.36        19.79        21.37        38.70 
TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W 
       64.96        63.75        21.04         1.64        50.70        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
        8.91        53.06        37.91        46.09        48.36         5.59 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZH-A8Y2 TCGA-ZU-A8S4 
       26.56         0.69         0.85        23.05         3.22 

$`DEL PEAK  4(4Q34.3) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-ZH-A8Y1 TCGA-3X-AAVA TCGA-3X-AAVC TCGA-4G-AAZT 
       11.15        13.22        12.66        14.63        23.31        13.81 
TCGA-W5-AA2H TCGA-W5-AA2U TCGA-W5-AA33 TCGA-W5-AA34 TCGA-ZD-A8I3 TCGA-ZH-A8Y5 
       35.41        20.61        47.64        18.25         5.56        40.41 
TCGA-ZH-A8Y6 
       17.06 

  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                         0.33                          5.56 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                        64.96                         47.64 
  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE 
                        24.36                         17.06 
[1] "0.3 - 65.0 (24.4)" "5.6 - 47.6 (17.1)"
[1] "hr=" "1.2"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  4(4Q34.3) MUTATED        12        7         0        2         1
  DEL PEAK  4(4Q34.3) WILD-TYPE       7        2         1        0         1
                               vv
clus                            STAGE IVB
  DEL PEAK  4(4Q34.3) MUTATED           1
  DEL PEAK  4(4Q34.3) WILD-TYPE         2
D7V3, multiclass
           clus
vv          DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  STAGE I                            12                             7
  STAGE II                            7                             2
  STAGE III                           0                             1
  STAGE IV                            2                             0
  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
  DEL PEAK  4(4Q34.3) MUTATED   12 10  1
  DEL PEAK  4(4Q34.3) WILD-TYPE  7  2  4
D7V4, multiclass
    clus
vv   DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  T1                          12                             7
  T2                          10                             2
  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
  DEL PEAK  4(4Q34.3) MUTATED   17  2
  DEL PEAK  4(4Q34.3) WILD-TYPE  9  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q34.3) MUTATED     17    2
  DEL PEAK  4(4Q34.3) WILD-TYPE    9    3
   clus
vv  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  0                          17                             9
  1                           2                             3
[1] 2 2
[1] FALSE
D7V6, binary
                               cls
clus                             0  1
  DEL PEAK  4(4Q34.3) MUTATED   17  3
  DEL PEAK  4(4Q34.3) WILD-TYPE 11  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q34.3) MUTATED     17    3
  DEL PEAK  4(4Q34.3) WILD-TYPE   11    2
   clus
vv  DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  0                          17                            11
  1                           3                             2
[1] 2 2
[1] FALSE
D7V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(4Q34.3) MUTATED   11 12
  DEL PEAK  4(4Q34.3) WILD-TYPE  9  4
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(4Q34.3) MUTATED     11   12
  DEL PEAK  4(4Q34.3) WILD-TYPE    9    4
        clus
vv       DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  FEMALE                          11                             9
  MALE                            12                             4
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  4(4Q34.3) MUTATED                            0
  DEL PEAK  4(4Q34.3) WILD-TYPE                          2
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  4(4Q34.3) MUTATED                                     3
  DEL PEAK  4(4Q34.3) WILD-TYPE                                   1
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  4(4Q34.3) MUTATED                                 20
  DEL PEAK  4(4Q34.3) WILD-TYPE                               10
D7V8, multiclass
                                     clus
vv                                    DEL PEAK  4(4Q34.3) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                             20
                                     clus
vv                                    DEL PEAK  4(4Q34.3) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               10
[1] 3 2
[1] 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
  DEL PEAK  4(4Q34.3) MUTATED   16  4  3
  DEL PEAK  4(4Q34.3) WILD-TYPE 12  1  0
D7V9, multiclass
    clus
vv   DEL PEAK  4(4Q34.3) MUTATED DEL PEAK  4(4Q34.3) WILD-TYPE
  R0                          16                            12
  R1                           4                             1
  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
  DEL PEAK  4(4Q34.3) MUTATED       1                         1    21
  DEL PEAK  4(4Q34.3) WILD-TYPE     2                         1    10
D7V10, multiclass
                           clus
vv                          DEL PEAK  4(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              21
                           clus
vv                          DEL PEAK  4(4Q34.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                10
[1] 3 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 = DEL PEAK  5(5Q13.3) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(5Q13.3) MUTATED    4  4
  DEL PEAK  5(5Q13.3) WILD-TYPE 14 14
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                            8                            28 
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                            4                            14 
$`DEL PEAK  5(5Q13.3) MUTATED`
TCGA-3X-AAVB TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2X TCGA-W5-AA30 TCGA-YR-A95A 
       13.22        23.31        21.37         8.91        37.91         0.85 
TCGA-ZH-A8Y2 TCGA-ZU-A8S4 
       23.05         3.22 

$`DEL PEAK  5(5Q13.3) WILD-TYPE`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I 
       14.63        38.70        13.81        64.96        35.41        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2Z 
       21.04         1.64        50.70        20.61        30.38        53.06 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       47.64        18.25        46.09        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.69         5.56        40.41        17.06 

  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                         0.85                          0.33 
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                        37.91                         64.96 
  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE 
                       17.295                        22.700 
[1] "0.8 - 37.9 (17.3)" "0.3 - 65.0 (22.7)"
[1] "hr=" "1.7"
D8V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  5(5Q13.3) MUTATED         4        1         0        1         0
  DEL PEAK  5(5Q13.3) WILD-TYPE      15        8         1        1         2
                               vv
clus                            STAGE IVB
  DEL PEAK  5(5Q13.3) MUTATED           2
  DEL PEAK  5(5Q13.3) WILD-TYPE         1
D8V3, multiclass
           clus
vv          DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE
  STAGE I                             4                            15
  STAGE II                            1                             8
  STAGE III                           0                             1
  STAGE IV                            1                             1
  STAGE IVA                           0                             2
  STAGE IVB                           2                             1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3
  DEL PEAK  5(5Q13.3) MUTATED    4  3  1
  DEL PEAK  5(5Q13.3) WILD-TYPE 15  9  4
D8V4, multiclass
    clus
vv   DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) 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"
D8V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(5Q13.3) MUTATED    3  2
  DEL PEAK  5(5Q13.3) WILD-TYPE 23  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5Q13.3) MUTATED      3    2
  DEL PEAK  5(5Q13.3) WILD-TYPE   23    3
   clus
vv  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE
  0                           3                            23
  1                           2                             3
[1] 2 2
[1] FALSE
D8V6, binary
                               cls
clus                             0  1
  DEL PEAK  5(5Q13.3) MUTATED    4  3
  DEL PEAK  5(5Q13.3) WILD-TYPE 24  2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5Q13.3) MUTATED      4    3
  DEL PEAK  5(5Q13.3) WILD-TYPE   24    2
   clus
vv  DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE
  0                           4                            24
  1                           3                             2
[1] 2 2
[1] FALSE
D8V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(5Q13.3) MUTATED    3  5
  DEL PEAK  5(5Q13.3) WILD-TYPE 17 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(5Q13.3) MUTATED      3    5
  DEL PEAK  5(5Q13.3) WILD-TYPE   17   11
        clus
vv       DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE
  FEMALE                           3                            17
  MALE                             5                            11
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  5(5Q13.3) MUTATED                            1
  DEL PEAK  5(5Q13.3) WILD-TYPE                          1
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  5(5Q13.3) MUTATED                                     3
  DEL PEAK  5(5Q13.3) WILD-TYPE                                   1
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  5(5Q13.3) MUTATED                                  4
  DEL PEAK  5(5Q13.3) WILD-TYPE                               26
D8V8, multiclass
                                     clus
vv                                    DEL PEAK  5(5Q13.3) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              4
                                     clus
vv                                    DEL PEAK  5(5Q13.3) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               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
  DEL PEAK  5(5Q13.3) MUTATED    6  1  1
  DEL PEAK  5(5Q13.3) WILD-TYPE 22  4  2
D8V9, multiclass
    clus
vv   DEL PEAK  5(5Q13.3) MUTATED DEL PEAK  5(5Q13.3) WILD-TYPE
  R0                           6                            22
  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
  DEL PEAK  5(5Q13.3) MUTATED       1                         1     6
  DEL PEAK  5(5Q13.3) WILD-TYPE     2                         1    25
D8V10, multiclass
                           clus
vv                          DEL PEAK  5(5Q13.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               6
                           clus
vv                          DEL PEAK  5(5Q13.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = DEL PEAK  6(6Q13) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  6(6Q13) MUTATED   10 11
  DEL PEAK  6(6Q13) WILD-TYPE  8  7
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                         21                          15 
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                         11                           7 
$`DEL PEAK  6(6Q13) MUTATED`
TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       13.22        40.11         0.33        24.36        19.79        14.63 
TCGA-4G-AAZT TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA30 
       13.81        63.75        21.04        20.61        53.06        37.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       47.64        18.25        48.36        26.56         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
        5.56        23.05        40.41 

$`DEL PEAK  6(6Q13) WILD-TYPE`
TCGA-3X-AAV9 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G 
       11.15        12.66        23.31        21.37        38.70        64.96 
TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA36 
       35.41         1.64        50.70        30.38         8.91        46.09 
TCGA-W5-AA39 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.59        17.06         3.22 

  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                       0.33                        1.64 
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                      63.75                       64.96 
  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE 
                      21.04                       21.37 
[1] "0.3 - 63.8 (21.0)" "1.6 - 65.0 (21.4)"
[1] "hr=" "1.1"
D9V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  6(6Q13) MUTATED        13        5         0        1         0
  DEL PEAK  6(6Q13) WILD-TYPE       6        4         1        1         2
                             vv
clus                          STAGE IVB
  DEL PEAK  6(6Q13) MUTATED           2
  DEL PEAK  6(6Q13) WILD-TYPE         1
D9V3, multiclass
           clus
vv          DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  STAGE I                          13                           6
  STAGE II                          5                           4
  STAGE III                         0                           1
  STAGE IV                          1                           1
  STAGE IVA                         0                           2
  STAGE IVB                         2                           1
[1] 6 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3
  DEL PEAK  6(6Q13) MUTATED   13  6  2
  DEL PEAK  6(6Q13) WILD-TYPE  6  6  3
D9V4, multiclass
    clus
vv   DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  T1                        13                           6
  T2                         6                           6
  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"
D9V5, binary
                             cls
clus                           0  1
  DEL PEAK  6(6Q13) MUTATED   15  2
  DEL PEAK  6(6Q13) WILD-TYPE 11  3
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q13) MUTATED     15    2
  DEL PEAK  6(6Q13) WILD-TYPE   11    3
   clus
vv  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  0                        15                          11
  1                         2                           3
[1] 2 2
[1] FALSE
D9V6, binary
                             cls
clus                           0  1
  DEL PEAK  6(6Q13) MUTATED   16  3
  DEL PEAK  6(6Q13) WILD-TYPE 12  2
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q13) MUTATED     16    3
  DEL PEAK  6(6Q13) WILD-TYPE   12    2
   clus
vv  DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  0                        16                          12
  1                         3                           2
[1] 2 2
[1] FALSE
D9V7, binary
                             cls
clus                           0  1
  DEL PEAK  6(6Q13) MUTATED   11 10
  DEL PEAK  6(6Q13) WILD-TYPE  9  6
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(6Q13) MUTATED     11   10
  DEL PEAK  6(6Q13) WILD-TYPE    9    6
        clus
vv       DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  FEMALE                        11                           9
  MALE                          10                           6
[1] 2 2
[1] FALSE
                             vv
clus                          CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  6(6Q13) MUTATED                            1
  DEL PEAK  6(6Q13) WILD-TYPE                          1
                             vv
clus                          CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  6(6Q13) MUTATED                                     1
  DEL PEAK  6(6Q13) WILD-TYPE                                   3
                             vv
clus                          CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  6(6Q13) MUTATED                                 19
  DEL PEAK  6(6Q13) WILD-TYPE                               11
D9V8, multiclass
                                     clus
vv                                    DEL PEAK  6(6Q13) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                  1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                         1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                           19
                                     clus
vv                                    DEL PEAK  6(6Q13) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                    1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                             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
  DEL PEAK  6(6Q13) MUTATED   17  3  1
  DEL PEAK  6(6Q13) WILD-TYPE 11  2  2
D9V9, multiclass
    clus
vv   DEL PEAK  6(6Q13) MUTATED DEL PEAK  6(6Q13) WILD-TYPE
  R0                        17                          11
  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
  DEL PEAK  6(6Q13) MUTATED       1                         1    19
  DEL PEAK  6(6Q13) WILD-TYPE     2                         1    12
D9V10, multiclass
                           clus
vv                          DEL PEAK  6(6Q13) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         1
  WHITE                                            19
                           clus
vv                          DEL PEAK  6(6Q13) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              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(10) Variable = DEL PEAK  7(9P21.3) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(9P21.3) MUTATED   10 13
  DEL PEAK  7(9P21.3) WILD-TYPE  8  5
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           23                            13 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                           13                             5 
$`DEL PEAK  7(9P21.3) MUTATED`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       11.15        13.22        40.11        24.36        19.79        14.63 
TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2U 
       23.31        21.37        38.70        64.96        63.75        20.61 
TCGA-W5-AA2W TCGA-W5-AA30 TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 
       30.38        37.91        47.64        18.25        46.09        48.36 
TCGA-W6-AA0S TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZU-A8S4 
       26.56         0.69         5.56        23.05         3.22 

$`DEL PEAK  7(9P21.3) WILD-TYPE`
TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q 
        0.33        12.66        13.81        35.41        21.04         1.64 
TCGA-W5-AA2R TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA39 TCGA-YR-A95A TCGA-ZH-A8Y5 
       50.70         8.91        53.06         5.59         0.85        40.41 
TCGA-ZH-A8Y6 
       17.06 

  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                         0.69                          0.33 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                        64.96                         53.06 
  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE 
                        23.31                         13.81 
[1] "0.7 - 65.0 (23.3)" "0.3 - 53.1 (13.8)"
[1] "hr=" "1"  
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  7(9P21.3) MUTATED        14        6         0        1         1
  DEL PEAK  7(9P21.3) WILD-TYPE       5        3         1        1         1
                               vv
clus                            STAGE IVB
  DEL PEAK  7(9P21.3) MUTATED           1
  DEL PEAK  7(9P21.3) WILD-TYPE         2
D10V3, multiclass
           clus
vv          DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  STAGE I                            14                             5
  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
  DEL PEAK  7(9P21.3) MUTATED   14  7  2
  DEL PEAK  7(9P21.3) WILD-TYPE  5  5  3
D10V4, multiclass
    clus
vv   DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  T1                          14                             5
  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"
D10V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED   17  2
  DEL PEAK  7(9P21.3) WILD-TYPE  9  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED     17    2
  DEL PEAK  7(9P21.3) WILD-TYPE    9    3
   clus
vv  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  0                          17                             9
  1                           2                             3
[1] 2 2
[1] FALSE
D10V6, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED   18  2
  DEL PEAK  7(9P21.3) WILD-TYPE 10  3
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED     18    2
  DEL PEAK  7(9P21.3) WILD-TYPE   10    3
   clus
vv  DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  0                          18                            10
  1                           2                             3
[1] 2 2
[1] FALSE
D10V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(9P21.3) MUTATED   15  8
  DEL PEAK  7(9P21.3) WILD-TYPE  5  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(9P21.3) MUTATED     15    8
  DEL PEAK  7(9P21.3) WILD-TYPE    5    8
        clus
vv       DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  FEMALE                          15                             5
  MALE                             8                             8
[1] 2 2
[1] FALSE
                               vv
clus                            CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  7(9P21.3) MUTATED                            1
  DEL PEAK  7(9P21.3) WILD-TYPE                          1
                               vv
clus                            CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  7(9P21.3) MUTATED                                     2
  DEL PEAK  7(9P21.3) WILD-TYPE                                   2
                               vv
clus                            CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  7(9P21.3) MUTATED                                 20
  DEL PEAK  7(9P21.3) WILD-TYPE                               10
D10V8, multiclass
                                     clus
vv                                    DEL PEAK  7(9P21.3) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                    1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                           2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                             20
                                     clus
vv                                    DEL PEAK  7(9P21.3) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                      1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             2
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               10
[1] 3 2
[1] 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
  DEL PEAK  7(9P21.3) MUTATED   20  2  1
  DEL PEAK  7(9P21.3) WILD-TYPE  8  3  2
D10V9, multiclass
    clus
vv   DEL PEAK  7(9P21.3) MUTATED DEL PEAK  7(9P21.3) WILD-TYPE
  R0                          20                             8
  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
  DEL PEAK  7(9P21.3) MUTATED       3                         1    19
  DEL PEAK  7(9P21.3) WILD-TYPE     0                         1    12
D10V10, multiclass
                           clus
vv                          DEL PEAK  7(9P21.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              19
                           clus
vv                          DEL PEAK  7(9P21.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                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(11) Variable = DEL PEAK  8(9Q21.11) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  8(9Q21.11) MUTATED    9 10
  DEL PEAK  8(9Q21.11) WILD-TYPE  9  8
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                            19                             17 
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                            10                              8 
$`DEL PEAK  8(9Q21.11) MUTATED`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVC 
       11.15        40.11        12.66        24.36        19.79        23.31 
TCGA-3X-AAVE TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2U TCGA-W5-AA30 
       21.37        38.70        64.96        63.75        20.61        37.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA38 TCGA-WD-A7RX TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       47.64        18.25        48.36         0.69         5.56        23.05 
TCGA-ZH-A8Y5 
       40.41 

$`DEL PEAK  8(9Q21.11) WILD-TYPE`
TCGA-3X-AAVB TCGA-W5-AA31 TCGA-3X-AAVA TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2O 
       13.22         0.33        14.63        13.81        35.41        21.04 
TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA36 
        1.64        50.70        30.38         8.91        53.06        46.09 
TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.59        26.56         0.85        17.06         3.22 

  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                          0.69                           0.33 
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                         64.96                          53.06 
  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE 
                         23.31                          14.63 
[1] "0.7 - 65.0 (23.3)" "0.3 - 53.1 (14.6)"
[1] "hr=" "1.4"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  8(9Q21.11) MUTATED        12        5         0        0         1
  DEL PEAK  8(9Q21.11) WILD-TYPE       7        4         1        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK  8(9Q21.11) MUTATED           1
  DEL PEAK  8(9Q21.11) WILD-TYPE         2
D11V3, multiclass
           clus
vv          DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  STAGE I                             12                              7
  STAGE II                             5                              4
  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
  DEL PEAK  8(9Q21.11) MUTATED   12  5  2
  DEL PEAK  8(9Q21.11) WILD-TYPE  7  7  3
D11V4, multiclass
    clus
vv   DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  T1                           12                              7
  T2                            5                              7
  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"
D11V5, binary
                                cls
clus                              0  1
  DEL PEAK  8(9Q21.11) MUTATED   15  2
  DEL PEAK  8(9Q21.11) WILD-TYPE 11  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(9Q21.11) MUTATED     15    2
  DEL PEAK  8(9Q21.11) WILD-TYPE   11    3
   clus
vv  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  0                           15                             11
  1                            2                              3
[1] 2 2
[1] FALSE
D11V6, binary
                                cls
clus                              0  1
  DEL PEAK  8(9Q21.11) MUTATED   17  1
  DEL PEAK  8(9Q21.11) WILD-TYPE 11  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(9Q21.11) MUTATED     17    1
  DEL PEAK  8(9Q21.11) WILD-TYPE   11    4
   clus
vv  DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  0                           17                             11
  1                            1                              4
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                              0  1
  DEL PEAK  8(9Q21.11) MUTATED   11  8
  DEL PEAK  8(9Q21.11) WILD-TYPE  9  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(9Q21.11) MUTATED     11    8
  DEL PEAK  8(9Q21.11) WILD-TYPE    9    8
        clus
vv       DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  FEMALE                           11                              9
  MALE                              8                              8
[1] 2 2
[1] FALSE
                                vv
clus                             CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  8(9Q21.11) MUTATED                            0
  DEL PEAK  8(9Q21.11) WILD-TYPE                          2
                                vv
clus                             CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  8(9Q21.11) MUTATED                                     1
  DEL PEAK  8(9Q21.11) WILD-TYPE                                   3
                                vv
clus                             CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  8(9Q21.11) MUTATED                                 18
  DEL PEAK  8(9Q21.11) WILD-TYPE                               12
D11V8, multiclass
                                     clus
vv                                    DEL PEAK  8(9Q21.11) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                     0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                            1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              18
                                     clus
vv                                    DEL PEAK  8(9Q21.11) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                       2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                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
  DEL PEAK  8(9Q21.11) MUTATED   15  3  1
  DEL PEAK  8(9Q21.11) WILD-TYPE 13  2  2
D11V9, multiclass
    clus
vv   DEL PEAK  8(9Q21.11) MUTATED DEL PEAK  8(9Q21.11) WILD-TYPE
  R0                           15                             13
  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
  DEL PEAK  8(9Q21.11) MUTATED       3                         1    15
  DEL PEAK  8(9Q21.11) WILD-TYPE     0                         1    16
D11V10, multiclass
                           clus
vv                          DEL PEAK  8(9Q21.11) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          DEL PEAK  8(9Q21.11) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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(12) Variable = DEL PEAK  9(10Q26.12) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK  9(10Q26.12) MUTATED    6  6
  DEL PEAK  9(10Q26.12) WILD-TYPE 12 12
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                             12                              24 
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                              6                              12 
$`DEL PEAK  9(10Q26.12) MUTATED`
TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-3X-AAVA TCGA-3X-AAVE 
       13.22         0.33        12.66        24.36        14.63        21.37 
TCGA-W5-AA2I TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-ZU-A8S4 
       63.75        50.70        30.38        53.06        37.91         3.22 

$`DEL PEAK  9(10Q26.12) WILD-TYPE`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-ZH-A8Y8 TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT 
       11.15        40.11        19.79        23.31        38.70        13.81 
TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2U TCGA-W5-AA2X 
       64.96        35.41        21.04         1.64        20.61         8.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-W6-AA0S 
       47.64        18.25        46.09        48.36         5.59        26.56 
TCGA-WD-A7RX TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.69         0.85         5.56        23.05        40.41        17.06 

  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                           0.33                            0.69 
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                          63.75                           64.96 
  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE 
                         22.865                          20.825 
[1] "0.3 - 63.8 (22.9)" "0.7 - 65.0 (20.8)"
[1] "hr=" "1.1"
D12V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK  9(10Q26.12) MUTATED         6        3         0        0         2
  DEL PEAK  9(10Q26.12) WILD-TYPE      13        6         1        2         0
                                 vv
clus                              STAGE IVB
  DEL PEAK  9(10Q26.12) MUTATED           1
  DEL PEAK  9(10Q26.12) WILD-TYPE         2
D12V3, multiclass
           clus
vv          DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  STAGE I                               6                              13
  STAGE II                              3                               6
  STAGE III                             0                               1
  STAGE IV                              0                               2
  STAGE IVA                             2                               0
  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
  DEL PEAK  9(10Q26.12) MUTATED    6  4  2
  DEL PEAK  9(10Q26.12) WILD-TYPE 13  8  3
D12V4, multiclass
    clus
vv   DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  T1                             6                              13
  T2                             4                               8
  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"
D12V5, binary
                                 cls
clus                               0  1
  DEL PEAK  9(10Q26.12) MUTATED    7  3
  DEL PEAK  9(10Q26.12) WILD-TYPE 19  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(10Q26.12) MUTATED      7    3
  DEL PEAK  9(10Q26.12) WILD-TYPE   19    2
   clus
vv  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  0                             7                              19
  1                             3                               2
[1] 2 2
[1] FALSE
D12V6, binary
                                 cls
clus                               0  1
  DEL PEAK  9(10Q26.12) MUTATED   10  1
  DEL PEAK  9(10Q26.12) WILD-TYPE 18  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(10Q26.12) MUTATED     10    1
  DEL PEAK  9(10Q26.12) WILD-TYPE   18    4
   clus
vv  DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  0                            10                              18
  1                             1                               4
[1] 2 2
[1] FALSE
D12V7, binary
                                 cls
clus                               0  1
  DEL PEAK  9(10Q26.12) MUTATED    6  6
  DEL PEAK  9(10Q26.12) WILD-TYPE 14 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK  9(10Q26.12) MUTATED      6    6
  DEL PEAK  9(10Q26.12) WILD-TYPE   14   10
        clus
vv       DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  FEMALE                             6                              14
  MALE                               6                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK  9(10Q26.12) MUTATED                            1
  DEL PEAK  9(10Q26.12) WILD-TYPE                          1
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK  9(10Q26.12) MUTATED                                     0
  DEL PEAK  9(10Q26.12) WILD-TYPE                                   4
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK  9(10Q26.12) MUTATED                                 11
  DEL PEAK  9(10Q26.12) WILD-TYPE                               19
D12V8, multiclass
                                     clus
vv                                    DEL PEAK  9(10Q26.12) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             0
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               11
                                     clus
vv                                    DEL PEAK  9(10Q26.12) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 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"
                                 vv
clus                              R0 R1 RX
  DEL PEAK  9(10Q26.12) MUTATED    9  3  0
  DEL PEAK  9(10Q26.12) WILD-TYPE 19  2  3
D12V9, multiclass
    clus
vv   DEL PEAK  9(10Q26.12) MUTATED DEL PEAK  9(10Q26.12) WILD-TYPE
  R0                             9                              19
  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
  DEL PEAK  9(10Q26.12) MUTATED       1                         0    11
  DEL PEAK  9(10Q26.12) WILD-TYPE     2                         2    20
D12V10, multiclass
                           clus
vv                          DEL PEAK  9(10Q26.12) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                11
                           clus
vv                          DEL PEAK  9(10Q26.12) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  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(13) Variable = DEL PEAK 10(11Q25) MUTATION ANALYSIS
D13V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 10(11Q25) MUTATED    4  9
  DEL PEAK 10(11Q25) WILD-TYPE 14  9
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                          13                           23 
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                           9                            9 
$`DEL PEAK 10(11Q25) MUTATED`
TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-3X-AAVC TCGA-3X-AAVE TCGA-W5-AA2O 
       40.11         0.33        24.36        23.31        21.37        21.04 
TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W5-AA30 TCGA-W5-AA34 TCGA-WD-A7RX TCGA-YR-A95A 
       20.61         8.91        37.91        18.25         0.69         0.85 
TCGA-ZH-A8Y2 
       23.05 

$`DEL PEAK 10(11Q25) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-4G-AAZO 
       11.15        13.22        12.66        19.79        14.63        38.70 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2Q TCGA-W5-AA2R 
       13.81        64.96        35.41        63.75         1.64        50.70 
TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 
       30.38        53.06        47.64        46.09        48.36         5.59 
TCGA-W6-AA0S TCGA-ZD-A8I3 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
       26.56         5.56        40.41        17.06         3.22 

  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                        0.33                         1.64 
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                       40.11                        64.96 
  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE 
                       21.04                        26.56 
[1] "0.3 - 40.1 (21.0)" "1.6 - 65.0 (26.6)"
[1] "hr=" "3"  
D13V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 10(11Q25) MUTATED         8        3         0        1         0
  DEL PEAK 10(11Q25) WILD-TYPE      11        6         1        1         2
                              vv
clus                           STAGE IVB
  DEL PEAK 10(11Q25) MUTATED           1
  DEL PEAK 10(11Q25) WILD-TYPE         2
D13V3, multiclass
           clus
vv          DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE
  STAGE I                            8                           11
  STAGE II                           3                            6
  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
  DEL PEAK 10(11Q25) MUTATED    8  5  0
  DEL PEAK 10(11Q25) WILD-TYPE 11  7  5
D13V4, multiclass
    clus
vv   DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) 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"
D13V5, binary
                              cls
clus                            0  1
  DEL PEAK 10(11Q25) MUTATED    9  1
  DEL PEAK 10(11Q25) WILD-TYPE 17  4
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(11Q25) MUTATED      9    1
  DEL PEAK 10(11Q25) WILD-TYPE   17    4
   clus
vv  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE
  0                          9                           17
  1                          1                            4
[1] 2 2
[1] FALSE
D13V6, binary
                              cls
clus                            0  1
  DEL PEAK 10(11Q25) MUTATED   10  2
  DEL PEAK 10(11Q25) WILD-TYPE 18  3
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(11Q25) MUTATED     10    2
  DEL PEAK 10(11Q25) WILD-TYPE   18    3
   clus
vv  DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE
  0                         10                           18
  1                          2                            3
[1] 2 2
[1] FALSE
D13V7, binary
                              cls
clus                            0  1
  DEL PEAK 10(11Q25) MUTATED    6  7
  DEL PEAK 10(11Q25) WILD-TYPE 14  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 10(11Q25) MUTATED      6    7
  DEL PEAK 10(11Q25) WILD-TYPE   14    9
        clus
vv       DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) WILD-TYPE
  FEMALE                          6                           14
  MALE                            7                            9
[1] 2 2
[1] FALSE
                              vv
clus                           CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 10(11Q25) MUTATED                            0
  DEL PEAK 10(11Q25) WILD-TYPE                          2
                              vv
clus                           CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 10(11Q25) MUTATED                                     3
  DEL PEAK 10(11Q25) WILD-TYPE                                   1
                              vv
clus                           CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 10(11Q25) MUTATED                                 10
  DEL PEAK 10(11Q25) WILD-TYPE                               20
D13V8, multiclass
                                     clus
vv                                    DEL PEAK 10(11Q25) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                   0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                          3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                            10
                                     clus
vv                                    DEL PEAK 10(11Q25) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                     2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                            1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              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
  DEL PEAK 10(11Q25) MUTATED    9  2  2
  DEL PEAK 10(11Q25) WILD-TYPE 19  3  1
D13V9, multiclass
    clus
vv   DEL PEAK 10(11Q25) MUTATED DEL PEAK 10(11Q25) 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
  DEL PEAK 10(11Q25) MUTATED       1                         1    11
  DEL PEAK 10(11Q25) WILD-TYPE     2                         1    20
D13V10, multiclass
                           clus
vv                          DEL PEAK 10(11Q25) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             11
                           clus
vv                          DEL PEAK 10(11Q25) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               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(14) Variable = DEL PEAK 11(12Q24.13) MUTATION ANALYSIS
D14V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 11(12Q24.13) MUTATED    5  3
  DEL PEAK 11(12Q24.13) WILD-TYPE 13 15
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                              8                              28 
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                              3                              15 
$`DEL PEAK 11(12Q24.13) MUTATED`
TCGA-3X-AAVB TCGA-4G-AAZO TCGA-W5-AA2G TCGA-W5-AA2U TCGA-W5-AA2X TCGA-W6-AA0S 
       13.22        38.70        64.96        20.61         8.91        26.56 
TCGA-WD-A7RX TCGA-ZH-A8Y5 
        0.69        40.41 

$`DEL PEAK 11(12Q24.13) WILD-TYPE`
TCGA-3X-AAV9 TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 
       11.15        40.11         0.33        12.66        24.36        19.79 
TCGA-3X-AAVA TCGA-3X-AAVC TCGA-3X-AAVE TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2I 
       14.63        23.31        21.37        13.81        35.41        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W TCGA-W5-AA2Z TCGA-W5-AA30 
       21.04         1.64        50.70        30.38        53.06        37.91 
TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W5-AA39 TCGA-YR-A95A 
       47.64        18.25        46.09        48.36         5.59         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        23.05        17.06         3.22 

  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                           0.69                            0.33 
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                          64.96                           63.75 
  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE 
                         23.585                          21.205 
[1] "0.7 - 65.0 (23.6)" "0.3 - 63.8 (21.2)"
[1] "hr=" "1.6"
D14V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 11(12Q24.13) MUTATED         3        2         0        0         0
  DEL PEAK 11(12Q24.13) WILD-TYPE      16        7         1        2         2
                                 vv
clus                              STAGE IVB
  DEL PEAK 11(12Q24.13) MUTATED           3
  DEL PEAK 11(12Q24.13) WILD-TYPE         0
D14V3, multiclass
           clus
vv          DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  STAGE I                               3                              16
  STAGE II                              2                               7
  STAGE III                             0                               1
  STAGE IV                              0                               2
  STAGE IVA                             0                               2
  STAGE IVB                             3                               0
[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
  DEL PEAK 11(12Q24.13) MUTATED    3  3  2
  DEL PEAK 11(12Q24.13) WILD-TYPE 16  9  3
D14V4, multiclass
    clus
vv   DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  T1                             3                              16
  T2                             3                               9
  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"
D14V5, binary
                                 cls
clus                               0  1
  DEL PEAK 11(12Q24.13) MUTATED    4  3
  DEL PEAK 11(12Q24.13) WILD-TYPE 22  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q24.13) MUTATED      4    3
  DEL PEAK 11(12Q24.13) WILD-TYPE   22    2
   clus
vv  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  0                             4                              22
  1                             3                               2
[1] 2 2
[1] FALSE
D14V6, binary
                                 cls
clus                               0  1
  DEL PEAK 11(12Q24.13) MUTATED    3  3
  DEL PEAK 11(12Q24.13) WILD-TYPE 25  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q24.13) MUTATED      3    3
  DEL PEAK 11(12Q24.13) WILD-TYPE   25    2
   clus
vv  DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  0                             3                              25
  1                             3                               2
[1] 2 2
[1] FALSE
D14V7, binary
                                 cls
clus                               0  1
  DEL PEAK 11(12Q24.13) MUTATED    6  2
  DEL PEAK 11(12Q24.13) WILD-TYPE 14 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(12Q24.13) MUTATED      6    2
  DEL PEAK 11(12Q24.13) WILD-TYPE   14   14
        clus
vv       DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  FEMALE                             6                              14
  MALE                               2                              14
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 11(12Q24.13) MUTATED                            1
  DEL PEAK 11(12Q24.13) WILD-TYPE                          1
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 11(12Q24.13) MUTATED                                     1
  DEL PEAK 11(12Q24.13) WILD-TYPE                                   3
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 11(12Q24.13) MUTATED                                  6
  DEL PEAK 11(12Q24.13) WILD-TYPE                               24
D14V8, multiclass
                                     clus
vv                                    DEL PEAK 11(12Q24.13) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                6
                                     clus
vv                                    DEL PEAK 11(12Q24.13) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        1
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 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
  DEL PEAK 11(12Q24.13) MUTATED    5  1  2
  DEL PEAK 11(12Q24.13) WILD-TYPE 23  4  1
D14V9, multiclass
    clus
vv   DEL PEAK 11(12Q24.13) MUTATED DEL PEAK 11(12Q24.13) WILD-TYPE
  R0                             5                              23
  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
  DEL PEAK 11(12Q24.13) MUTATED       0                         0     8
  DEL PEAK 11(12Q24.13) WILD-TYPE     3                         2    23
D14V10, multiclass
                           clus
vv                          DEL PEAK 11(12Q24.13) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 8
                           clus
vv                          DEL PEAK 11(12Q24.13) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  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(15) Variable = DEL PEAK 12(13Q21.32) MUTATION ANALYSIS
D15V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 12(13Q21.32) MUTATED    8  8
  DEL PEAK 12(13Q21.32) WILD-TYPE 10 10
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                             16                              20 
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                              8                              10 
$`DEL PEAK 12(13Q21.32) MUTATED`
TCGA-W5-AA2T TCGA-ZH-A8Y1 TCGA-ZH-A8Y8 TCGA-3X-AAVE TCGA-W5-AA2G TCGA-W5-AA2I 
       40.11        12.66        19.79        21.37        64.96        63.75 
TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA33 
       21.04        50.70        20.61        53.06        37.91        47.64 
TCGA-W5-AA34 TCGA-W5-AA38 TCGA-WD-A7RX TCGA-ZU-A8S4 
       18.25        48.36         0.69         3.22 

$`DEL PEAK 12(13Q21.32) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y4 TCGA-3X-AAVA TCGA-3X-AAVC 
       11.15        13.22         0.33        24.36        14.63        23.31 
TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2H TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X 
       38.70        13.81        35.41         1.64        30.38         8.91 
TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y2 
       46.09         5.59        26.56         0.85         5.56        23.05 
TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
       40.41        17.06 

  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                           0.69                            0.33 
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                          64.96                           46.09 
  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE 
                         29.640                          15.845 
[1] "0.7 - 65.0 (29.6)" "0.3 - 46.1 (15.8)"
[1] "hr=" "1.8"
D15V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 12(13Q21.32) MUTATED        11        4         0        0         1
  DEL PEAK 12(13Q21.32) WILD-TYPE       8        5         1        2         1
                                 vv
clus                              STAGE IVB
  DEL PEAK 12(13Q21.32) MUTATED           0
  DEL PEAK 12(13Q21.32) WILD-TYPE         3
D15V3, multiclass
           clus
vv          DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  STAGE I                              11                               8
  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
  DEL PEAK 12(13Q21.32) MUTATED   11  4  1
  DEL PEAK 12(13Q21.32) WILD-TYPE  8  8  4
D15V4, multiclass
    clus
vv   DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  T1                            11                               8
  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"
D15V5, binary
                                 cls
clus                               0  1
  DEL PEAK 12(13Q21.32) MUTATED   13  1
  DEL PEAK 12(13Q21.32) WILD-TYPE 13  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(13Q21.32) MUTATED     13    1
  DEL PEAK 12(13Q21.32) WILD-TYPE   13    4
   clus
vv  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  0                            13                              13
  1                             1                               4
[1] 2 2
[1] FALSE
D15V6, binary
                                 cls
clus                               0  1
  DEL PEAK 12(13Q21.32) MUTATED   14  0
  DEL PEAK 12(13Q21.32) WILD-TYPE 14  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(13Q21.32) MUTATED     14    0
  DEL PEAK 12(13Q21.32) WILD-TYPE   14    5
   clus
vv  DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  0                            14                              14
  1                             0                               5
[1] 2 2
[1] FALSE
D15V7, binary
                                 cls
clus                               0  1
  DEL PEAK 12(13Q21.32) MUTATED    9  7
  DEL PEAK 12(13Q21.32) WILD-TYPE 11  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 12(13Q21.32) MUTATED      9    7
  DEL PEAK 12(13Q21.32) WILD-TYPE   11    9
        clus
vv       DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  FEMALE                             9                              11
  MALE                               7                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 12(13Q21.32) MUTATED                            0
  DEL PEAK 12(13Q21.32) WILD-TYPE                          2
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 12(13Q21.32) MUTATED                                     0
  DEL PEAK 12(13Q21.32) WILD-TYPE                                   4
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 12(13Q21.32) MUTATED                                 16
  DEL PEAK 12(13Q21.32) WILD-TYPE                               14
D15V8, multiclass
                                     clus
vv                                    DEL PEAK 12(13Q21.32) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             0
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               16
                                     clus
vv                                    DEL PEAK 12(13Q21.32) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 14
[1] 3 2
[1] 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
  DEL PEAK 12(13Q21.32) MUTATED   13  2  1
  DEL PEAK 12(13Q21.32) WILD-TYPE 15  3  2
D15V9, multiclass
    clus
vv   DEL PEAK 12(13Q21.32) MUTATED DEL PEAK 12(13Q21.32) WILD-TYPE
  R0                            13                              15
  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
  DEL PEAK 12(13Q21.32) MUTATED       1                         0    15
  DEL PEAK 12(13Q21.32) WILD-TYPE     2                         2    16
D15V10, multiclass
                           clus
vv                          DEL PEAK 12(13Q21.32) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                15
                           clus
vv                          DEL PEAK 12(13Q21.32) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  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(16) Variable = DEL PEAK 13(14Q22.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(14Q22.1) MUTATED    6  8
  DEL PEAK 13(14Q22.1) WILD-TYPE 12 10
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                            14                             22 
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                             8                             10 
$`DEL PEAK 13(14Q22.1) MUTATED`
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO 
       40.11        24.36        19.79        14.63        21.37        38.70 
TCGA-4G-AAZT TCGA-W5-AA2U TCGA-W5-AA30 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-WD-A7RX 
       13.81        20.61        37.91        46.09        48.36         0.69 
TCGA-ZH-A8Y2 TCGA-ZU-A8S4 
       23.05         3.22 

$`DEL PEAK 13(14Q22.1) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-W5-AA2G 
       11.15        13.22         0.33        12.66        23.31        64.96 
TCGA-W5-AA2H TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2W 
       35.41        63.75        21.04         1.64        50.70        30.38 
TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA34 TCGA-W5-AA39 TCGA-W6-AA0S 
        8.91        53.06        47.64        18.25         5.59        26.56 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 
        0.85         5.56        40.41        17.06 

  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                          0.69                           0.33 
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                         48.36                          64.96 
  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE 
                        22.210                         19.645 
[1] "0.7 - 48.4 (22.2)" "0.3 - 65.0 (19.6)"
[1] "hr=" "1.3"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 13(14Q22.1) MUTATED         8        5         0        1         0
  DEL PEAK 13(14Q22.1) WILD-TYPE      11        4         1        1         2
                                vv
clus                             STAGE IVB
  DEL PEAK 13(14Q22.1) MUTATED           0
  DEL PEAK 13(14Q22.1) WILD-TYPE         3
D16V3, multiclass
           clus
vv          DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  STAGE I                              8                             11
  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
  DEL PEAK 13(14Q22.1) MUTATED    8  5  1
  DEL PEAK 13(14Q22.1) WILD-TYPE 11  7  4
D16V4, multiclass
    clus
vv   DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  T1                            8                             11
  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"
D16V5, binary
                                cls
clus                              0  1
  DEL PEAK 13(14Q22.1) MUTATED   10  0
  DEL PEAK 13(14Q22.1) WILD-TYPE 16  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(14Q22.1) MUTATED     10    0
  DEL PEAK 13(14Q22.1) WILD-TYPE   16    5
   clus
vv  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  0                           10                             16
  1                            0                              5
[1] 2 2
[1] FALSE
D16V6, binary
                                cls
clus                              0  1
  DEL PEAK 13(14Q22.1) MUTATED   11  1
  DEL PEAK 13(14Q22.1) WILD-TYPE 17  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(14Q22.1) MUTATED     11    1
  DEL PEAK 13(14Q22.1) WILD-TYPE   17    4
   clus
vv  DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  0                           11                             17
  1                            1                              4
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                              0  1
  DEL PEAK 13(14Q22.1) MUTATED    8  6
  DEL PEAK 13(14Q22.1) WILD-TYPE 12 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(14Q22.1) MUTATED      8    6
  DEL PEAK 13(14Q22.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  FEMALE                            8                             12
  MALE                              6                             10
[1] 2 2
[1] FALSE
                                vv
clus                             CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 13(14Q22.1) MUTATED                            0
  DEL PEAK 13(14Q22.1) WILD-TYPE                          2
                                vv
clus                             CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 13(14Q22.1) MUTATED                                     1
  DEL PEAK 13(14Q22.1) WILD-TYPE                                   3
                                vv
clus                             CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 13(14Q22.1) MUTATED                                 13
  DEL PEAK 13(14Q22.1) WILD-TYPE                               17
D16V8, multiclass
                                     clus
vv                                    DEL PEAK 13(14Q22.1) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                     0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                            1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                              13
                                     clus
vv                                    DEL PEAK 13(14Q22.1) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                       2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                              3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                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
  DEL PEAK 13(14Q22.1) MUTATED   11  2  1
  DEL PEAK 13(14Q22.1) WILD-TYPE 17  3  2
D16V9, multiclass
    clus
vv   DEL PEAK 13(14Q22.1) MUTATED DEL PEAK 13(14Q22.1) WILD-TYPE
  R0                           11                             17
  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
  DEL PEAK 13(14Q22.1) MUTATED       1                         1    12
  DEL PEAK 13(14Q22.1) WILD-TYPE     2                         1    19
D16V10, multiclass
                           clus
vv                          DEL PEAK 13(14Q22.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               12
                           clus
vv                          DEL PEAK 13(14Q22.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 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(17) Variable = DEL PEAK 14(14Q32.11) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 14(14Q32.11) MUTATED   10 10
  DEL PEAK 14(14Q32.11) WILD-TYPE  8  8
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                             20                              16 
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                             10                               8 
$`DEL PEAK 14(14Q32.11) MUTATED`
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO 
       40.11        24.36        19.79        14.63        21.37        38.70 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2U 
       13.81        64.96        63.75        21.04        50.70        20.61 
TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX 
       37.91        18.25        46.09        48.36        26.56         0.69 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       23.05        40.41 

$`DEL PEAK 14(14Q32.11) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-W5-AA2H 
       11.15        13.22         0.33        12.66        23.31        35.41 
TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA39 
        1.64        30.38         8.91        53.06        47.64         5.59 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.85         5.56        17.06         3.22 

  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                           0.69                            0.33 
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                          64.96                           53.06 
  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE 
                         25.460                          11.905 
[1] "0.7 - 65.0 (25.5)" "0.3 - 53.1 (11.9)"
[1] "hr=" "2"  
D17V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 14(14Q32.11) MUTATED        13        5         0        1         0
  DEL PEAK 14(14Q32.11) WILD-TYPE       6        4         1        1         2
                                 vv
clus                              STAGE IVB
  DEL PEAK 14(14Q32.11) MUTATED           1
  DEL PEAK 14(14Q32.11) WILD-TYPE         2
D17V3, multiclass
           clus
vv          DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  STAGE I                              13                               6
  STAGE II                              5                               4
  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
  DEL PEAK 14(14Q32.11) MUTATED   13  5  2
  DEL PEAK 14(14Q32.11) WILD-TYPE  6  7  3
D17V4, multiclass
    clus
vv   DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  T1                            13                               6
  T2                             5                               7
  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"
D17V5, binary
                                 cls
clus                               0  1
  DEL PEAK 14(14Q32.11) MUTATED   16  1
  DEL PEAK 14(14Q32.11) WILD-TYPE 10  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(14Q32.11) MUTATED     16    1
  DEL PEAK 14(14Q32.11) WILD-TYPE   10    4
   clus
vv  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  0                            16                              10
  1                             1                               4
[1] 2 2
[1] FALSE
D17V6, binary
                                 cls
clus                               0  1
  DEL PEAK 14(14Q32.11) MUTATED   16  2
  DEL PEAK 14(14Q32.11) WILD-TYPE 12  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(14Q32.11) MUTATED     16    2
  DEL PEAK 14(14Q32.11) WILD-TYPE   12    3
   clus
vv  DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  0                            16                              12
  1                             2                               3
[1] 2 2
[1] FALSE
D17V7, binary
                                 cls
clus                               0  1
  DEL PEAK 14(14Q32.11) MUTATED   12  8
  DEL PEAK 14(14Q32.11) WILD-TYPE  8  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 14(14Q32.11) MUTATED     12    8
  DEL PEAK 14(14Q32.11) WILD-TYPE    8    8
        clus
vv       DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  FEMALE                            12                               8
  MALE                               8                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 14(14Q32.11) MUTATED                            0
  DEL PEAK 14(14Q32.11) WILD-TYPE                          2
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 14(14Q32.11) MUTATED                                     1
  DEL PEAK 14(14Q32.11) WILD-TYPE                                   3
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 14(14Q32.11) MUTATED                                 19
  DEL PEAK 14(14Q32.11) WILD-TYPE                               11
D17V8, multiclass
                                     clus
vv                                    DEL PEAK 14(14Q32.11) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               19
                                     clus
vv                                    DEL PEAK 14(14Q32.11) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 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
  DEL PEAK 14(14Q32.11) MUTATED   17  2  1
  DEL PEAK 14(14Q32.11) WILD-TYPE 11  3  2
D17V9, multiclass
    clus
vv   DEL PEAK 14(14Q32.11) MUTATED DEL PEAK 14(14Q32.11) WILD-TYPE
  R0                            17                              11
  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
  DEL PEAK 14(14Q32.11) MUTATED       1                         1    18
  DEL PEAK 14(14Q32.11) WILD-TYPE     2                         1    13
D17V10, multiclass
                           clus
vv                          DEL PEAK 14(14Q32.11) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                18
                           clus
vv                          DEL PEAK 14(14Q32.11) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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(18) Variable = DEL PEAK 15(14Q32.13) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(14Q32.13) MUTATED   10 10
  DEL PEAK 15(14Q32.13) WILD-TYPE  8  8
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                             20                              16 
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                             10                               8 
$`DEL PEAK 15(14Q32.13) MUTATED`
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO 
       40.11        24.36        19.79        14.63        21.37        38.70 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2U 
       13.81        64.96        63.75        21.04        50.70        20.61 
TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX 
       37.91        18.25        46.09        48.36        26.56         0.69 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       23.05        40.41 

$`DEL PEAK 15(14Q32.13) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-W5-AA2H 
       11.15        13.22         0.33        12.66        23.31        35.41 
TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA39 
        1.64        30.38         8.91        53.06        47.64         5.59 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.85         5.56        17.06         3.22 

  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                           0.69                            0.33 
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                          64.96                           53.06 
  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE 
                         25.460                          11.905 
[1] "0.7 - 65.0 (25.5)" "0.3 - 53.1 (11.9)"
[1] "hr=" "2"  
D18V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 15(14Q32.13) MUTATED        13        5         0        1         0
  DEL PEAK 15(14Q32.13) WILD-TYPE       6        4         1        1         2
                                 vv
clus                              STAGE IVB
  DEL PEAK 15(14Q32.13) MUTATED           1
  DEL PEAK 15(14Q32.13) WILD-TYPE         2
D18V3, multiclass
           clus
vv          DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  STAGE I                              13                               6
  STAGE II                              5                               4
  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
  DEL PEAK 15(14Q32.13) MUTATED   13  5  2
  DEL PEAK 15(14Q32.13) WILD-TYPE  6  7  3
D18V4, multiclass
    clus
vv   DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  T1                            13                               6
  T2                             5                               7
  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"
D18V5, binary
                                 cls
clus                               0  1
  DEL PEAK 15(14Q32.13) MUTATED   16  1
  DEL PEAK 15(14Q32.13) WILD-TYPE 10  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(14Q32.13) MUTATED     16    1
  DEL PEAK 15(14Q32.13) WILD-TYPE   10    4
   clus
vv  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  0                            16                              10
  1                             1                               4
[1] 2 2
[1] FALSE
D18V6, binary
                                 cls
clus                               0  1
  DEL PEAK 15(14Q32.13) MUTATED   16  2
  DEL PEAK 15(14Q32.13) WILD-TYPE 12  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(14Q32.13) MUTATED     16    2
  DEL PEAK 15(14Q32.13) WILD-TYPE   12    3
   clus
vv  DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  0                            16                              12
  1                             2                               3
[1] 2 2
[1] FALSE
D18V7, binary
                                 cls
clus                               0  1
  DEL PEAK 15(14Q32.13) MUTATED   12  8
  DEL PEAK 15(14Q32.13) WILD-TYPE  8  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(14Q32.13) MUTATED     12    8
  DEL PEAK 15(14Q32.13) WILD-TYPE    8    8
        clus
vv       DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  FEMALE                            12                               8
  MALE                               8                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 15(14Q32.13) MUTATED                            0
  DEL PEAK 15(14Q32.13) WILD-TYPE                          2
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 15(14Q32.13) MUTATED                                     1
  DEL PEAK 15(14Q32.13) WILD-TYPE                                   3
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 15(14Q32.13) MUTATED                                 19
  DEL PEAK 15(14Q32.13) WILD-TYPE                               11
D18V8, multiclass
                                     clus
vv                                    DEL PEAK 15(14Q32.13) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               19
                                     clus
vv                                    DEL PEAK 15(14Q32.13) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 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
  DEL PEAK 15(14Q32.13) MUTATED   17  2  1
  DEL PEAK 15(14Q32.13) WILD-TYPE 11  3  2
D18V9, multiclass
    clus
vv   DEL PEAK 15(14Q32.13) MUTATED DEL PEAK 15(14Q32.13) WILD-TYPE
  R0                            17                              11
  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
  DEL PEAK 15(14Q32.13) MUTATED       1                         1    18
  DEL PEAK 15(14Q32.13) WILD-TYPE     2                         1    13
D18V10, multiclass
                           clus
vv                          DEL PEAK 15(14Q32.13) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                18
                           clus
vv                          DEL PEAK 15(14Q32.13) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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(19) Variable = DEL PEAK 16(14Q32.33) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(14Q32.33) MUTATED   10 10
  DEL PEAK 16(14Q32.33) WILD-TYPE  8  8
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                             20                              16 
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                             10                               8 
$`DEL PEAK 16(14Q32.33) MUTATED`
TCGA-W5-AA2T TCGA-ZH-A8Y4 TCGA-ZH-A8Y8 TCGA-3X-AAVA TCGA-3X-AAVE TCGA-4G-AAZO 
       40.11        24.36        19.79        14.63        21.37        38.70 
TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2I TCGA-W5-AA2O TCGA-W5-AA2R TCGA-W5-AA2U 
       13.81        64.96        63.75        21.04        50.70        20.61 
TCGA-W5-AA30 TCGA-W5-AA34 TCGA-W5-AA36 TCGA-W5-AA38 TCGA-W6-AA0S TCGA-WD-A7RX 
       37.91        18.25        46.09        48.36        26.56         0.69 
TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 
       23.05        40.41 

$`DEL PEAK 16(14Q32.33) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA31 TCGA-ZH-A8Y1 TCGA-3X-AAVC TCGA-W5-AA2H 
       11.15        13.22         0.33        12.66        23.31        35.41 
TCGA-W5-AA2Q TCGA-W5-AA2W TCGA-W5-AA2X TCGA-W5-AA2Z TCGA-W5-AA33 TCGA-W5-AA39 
        1.64        30.38         8.91        53.06        47.64         5.59 
TCGA-YR-A95A TCGA-ZD-A8I3 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        0.85         5.56        17.06         3.22 

  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                           0.69                            0.33 
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                          64.96                           53.06 
  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE 
                         25.460                          11.905 
[1] "0.7 - 65.0 (25.5)" "0.3 - 53.1 (11.9)"
[1] "hr=" "2"  
D19V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 16(14Q32.33) MUTATED        13        5         0        1         0
  DEL PEAK 16(14Q32.33) WILD-TYPE       6        4         1        1         2
                                 vv
clus                              STAGE IVB
  DEL PEAK 16(14Q32.33) MUTATED           1
  DEL PEAK 16(14Q32.33) WILD-TYPE         2
D19V3, multiclass
           clus
vv          DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  STAGE I                              13                               6
  STAGE II                              5                               4
  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
  DEL PEAK 16(14Q32.33) MUTATED   13  5  2
  DEL PEAK 16(14Q32.33) WILD-TYPE  6  7  3
D19V4, multiclass
    clus
vv   DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  T1                            13                               6
  T2                             5                               7
  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"
D19V5, binary
                                 cls
clus                               0  1
  DEL PEAK 16(14Q32.33) MUTATED   16  1
  DEL PEAK 16(14Q32.33) WILD-TYPE 10  4
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(14Q32.33) MUTATED     16    1
  DEL PEAK 16(14Q32.33) WILD-TYPE   10    4
   clus
vv  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  0                            16                              10
  1                             1                               4
[1] 2 2
[1] FALSE
D19V6, binary
                                 cls
clus                               0  1
  DEL PEAK 16(14Q32.33) MUTATED   16  2
  DEL PEAK 16(14Q32.33) WILD-TYPE 12  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(14Q32.33) MUTATED     16    2
  DEL PEAK 16(14Q32.33) WILD-TYPE   12    3
   clus
vv  DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  0                            16                              12
  1                             2                               3
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                               0  1
  DEL PEAK 16(14Q32.33) MUTATED   12  8
  DEL PEAK 16(14Q32.33) WILD-TYPE  8  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(14Q32.33) MUTATED     12    8
  DEL PEAK 16(14Q32.33) WILD-TYPE    8    8
        clus
vv       DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  FEMALE                            12                               8
  MALE                               8                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 16(14Q32.33) MUTATED                            0
  DEL PEAK 16(14Q32.33) WILD-TYPE                          2
                                 vv
clus                              CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 16(14Q32.33) MUTATED                                     1
  DEL PEAK 16(14Q32.33) WILD-TYPE                                   3
                                 vv
clus                              CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 16(14Q32.33) MUTATED                                 19
  DEL PEAK 16(14Q32.33) WILD-TYPE                               11
D19V8, multiclass
                                     clus
vv                                    DEL PEAK 16(14Q32.33) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                      0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                             1
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               19
                                     clus
vv                                    DEL PEAK 16(14Q32.33) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                        2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                               3
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                 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
  DEL PEAK 16(14Q32.33) MUTATED   17  2  1
  DEL PEAK 16(14Q32.33) WILD-TYPE 11  3  2
D19V9, multiclass
    clus
vv   DEL PEAK 16(14Q32.33) MUTATED DEL PEAK 16(14Q32.33) WILD-TYPE
  R0                            17                              11
  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
  DEL PEAK 16(14Q32.33) MUTATED       1                         1    18
  DEL PEAK 16(14Q32.33) WILD-TYPE     2                         1    13
D19V10, multiclass
                           clus
vv                          DEL PEAK 16(14Q32.33) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                18
                           clus
vv                          DEL PEAK 16(14Q32.33) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  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(20) Variable = DEL PEAK 17(16Q23.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(16Q23.1) MUTATED    4  3
  DEL PEAK 17(16Q23.1) WILD-TYPE 14 15
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             7                             29 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             3                             15 
$`DEL PEAK 17(16Q23.1) MUTATED`
TCGA-ZH-A8Y1 TCGA-ZH-A8Y4 TCGA-3X-AAVE TCGA-W5-AA2Z TCGA-W5-AA30 TCGA-W5-AA34 
       12.66        24.36        21.37        53.06        37.91        18.25 
TCGA-W5-AA38 
       48.36 

$`DEL PEAK 17(16Q23.1) WILD-TYPE`
TCGA-3X-AAV9 TCGA-3X-AAVB TCGA-W5-AA2T TCGA-W5-AA31 TCGA-ZH-A8Y8 TCGA-3X-AAVA 
       11.15        13.22        40.11         0.33        19.79        14.63 
TCGA-3X-AAVC TCGA-4G-AAZO TCGA-4G-AAZT TCGA-W5-AA2G TCGA-W5-AA2H TCGA-W5-AA2I 
       23.31        38.70        13.81        64.96        35.41        63.75 
TCGA-W5-AA2O TCGA-W5-AA2Q TCGA-W5-AA2R TCGA-W5-AA2U TCGA-W5-AA2W TCGA-W5-AA2X 
       21.04         1.64        50.70        20.61        30.38         8.91 
TCGA-W5-AA33 TCGA-W5-AA36 TCGA-W5-AA39 TCGA-W6-AA0S TCGA-WD-A7RX TCGA-YR-A95A 
       47.64        46.09         5.59        26.56         0.69         0.85 
TCGA-ZD-A8I3 TCGA-ZH-A8Y2 TCGA-ZH-A8Y5 TCGA-ZH-A8Y6 TCGA-ZU-A8S4 
        5.56        23.05        40.41        17.06         3.22 

  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         12.66                           0.33 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         53.06                          64.96 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         24.36                          20.61 
[1] "12.7 - 53.1 (24.4)" "0.3 - 65.0 (20.6)" 
[1] "hr=" "1.5"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV STAGE IVA
  DEL PEAK 17(16Q23.1) MUTATED         4        2         0        0         1
  DEL PEAK 17(16Q23.1) WILD-TYPE      15        7         1        2         1
                                vv
clus                             STAGE IVB
  DEL PEAK 17(16Q23.1) MUTATED           0
  DEL PEAK 17(16Q23.1) WILD-TYPE         3
D20V3, multiclass
           clus
vv          DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) 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
  DEL PEAK 17(16Q23.1) MUTATED    4  2  1
  DEL PEAK 17(16Q23.1) WILD-TYPE 15 10  4
D20V4, multiclass
    clus
vv   DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) 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"
D20V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    6  1
  DEL PEAK 17(16Q23.1) WILD-TYPE 20  4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      6    1
  DEL PEAK 17(16Q23.1) WILD-TYPE   20    4
   clus
vv  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  0                            6                             20
  1                            1                              4
[1] 2 2
[1] FALSE
D20V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    7  0
  DEL PEAK 17(16Q23.1) WILD-TYPE 21  5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      7    0
  DEL PEAK 17(16Q23.1) WILD-TYPE   21    5
   clus
vv  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  0                            7                             21
  1                            0                              5
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    4  3
  DEL PEAK 17(16Q23.1) WILD-TYPE 16 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      4    3
  DEL PEAK 17(16Q23.1) WILD-TYPE   16   13
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  FEMALE                            4                             16
  MALE                              3                             13
[1] 2 2
[1] FALSE
                                vv
clus                             CHOLANGIOCARCINOMA; DISTAL
  DEL PEAK 17(16Q23.1) MUTATED                            0
  DEL PEAK 17(16Q23.1) WILD-TYPE                          2
                                vv
clus                             CHOLANGIOCARCINOMA; HILAR/PERIHILAR
  DEL PEAK 17(16Q23.1) MUTATED                                     0
  DEL PEAK 17(16Q23.1) WILD-TYPE                                   4
                                vv
clus                             CHOLANGIOCARCINOMA; INTRAHEPATIC
  DEL PEAK 17(16Q23.1) MUTATED                                  7
  DEL PEAK 17(16Q23.1) WILD-TYPE                               23
D20V8, multiclass
                                     clus
vv                                    DEL PEAK 17(16Q23.1) MUTATED
  CHOLANGIOCARCINOMA; DISTAL                                     0
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                            0
  CHOLANGIOCARCINOMA; INTRAHEPATIC                               7
                                     clus
vv                                    DEL PEAK 17(16Q23.1) WILD-TYPE
  CHOLANGIOCARCINOMA; DISTAL                                       2
  CHOLANGIOCARCINOMA; HILAR/PERIHILAR                              4
  CHOLANGIOCARCINOMA; INTRAHEPATIC                                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
  DEL PEAK 17(16Q23.1) MUTATED    4  3  0
  DEL PEAK 17(16Q23.1) WILD-TYPE 24  2  3
D20V9, multiclass
    clus
vv   DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) 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
  DEL PEAK 17(16Q23.1) MUTATED       1                         0     6
  DEL PEAK 17(16Q23.1) WILD-TYPE     2                         2    25
D20V10, multiclass
                           clus
vv                          DEL PEAK 17(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          DEL PEAK 17(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 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"
