[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTLIHC-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/LIHC-TP/11541458/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/11562038/transformed.cor.cli.txt"

nPatients in clinical file=317, in cluster file=198, common to both=188
[1]  18 188
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            58            130 
  TP53 MUTATED TP53 WILD-TYPE 
            58            130 
[1] "CTNNB1 MUTATION ANALYSIS"
[1] 3
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              49              139 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              49              139 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           15           173 
  RB1 MUTATED RB1 WILD-TYPE 
           15           173 
[1] "AXIN1 MUTATION ANALYSIS"
[1] 3
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             179 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              9             179 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            178 
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            178 
[1] "TSC2 MUTATION ANALYSIS"
[1] 3
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            179 
  TSC2 MUTATED TSC2 WILD-TYPE 
             9            179 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              174 
  ARID1A MUTATED ARID1A WILD-TYPE 
              14              174 
[1] "IL6ST MUTATION ANALYSIS"
[1] 3
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             181 
  IL6ST MUTATED IL6ST WILD-TYPE 
              7             181 
[1] "ALB MUTATION ANALYSIS"
[1] 3
  ALB MUTATED ALB WILD-TYPE 
           18           170 
  ALB MUTATED ALB WILD-TYPE 
           18           170 
[1] "HNF1A MUTATION ANALYSIS"
[1] 3
  HNF1A MUTATED HNF1A WILD-TYPE 
              6             182 
  HNF1A MUTATED HNF1A WILD-TYPE 
              6             182 
[1] "APOB MUTATION ANALYSIS"
[1] 3
  APOB MUTATED APOB WILD-TYPE 
            23            165 
  APOB MUTATED APOB WILD-TYPE 
            23            165 
[1] "EEF1A1 MUTATION ANALYSIS"
[1] 3
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              183 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              183 
[1] "KIF19 MUTATION ANALYSIS"
[1] 3
  KIF19 MUTATED KIF19 WILD-TYPE 
              9             179 
  KIF19 MUTATED KIF19 WILD-TYPE 
              9             179 
[1] "GNAS MUTATION ANALYSIS"
[1] 3
  GNAS MUTATED GNAS WILD-TYPE 
             7            181 
  GNAS MUTATED GNAS WILD-TYPE 
             7            181 
[1] "F5 MUTATION ANALYSIS"
[1] 3
  F5 MUTATED F5 WILD-TYPE 
           4          184 
  F5 MUTATED F5 WILD-TYPE 
           4          184 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
             5            183 
  PTEN MUTATED PTEN WILD-TYPE 
             5            183 
[1] "HIST1H1C MUTATION ANALYSIS"
[1] 3
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                183 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                183 
[1] "DLK2 MUTATION ANALYSIS"
[1] 3
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            184 
  DLK2 MUTATED DLK2 WILD-TYPE 
             4            184 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 188 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
         849           NA           NA           NA           NA           NA 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
          NA           NA           NA           NA           NA         1351 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
         421            8          680          289          444          409 
TCGA-BW-A5NO TCGA-BW-A5NP TCGA-BW-A5NQ TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
          20           NA           NA            2            5           NA 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT 
          12           NA           NA           NA           NA           NA 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE 
           3            2            3            4           NA           NA 
TCGA-CC-A7IF TCGA-CC-A7IG TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A7IL TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
          NA         2425           NA           NA           NA         3437 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
          NA           79           NA          662           NA           NA 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG 
        2415         2017          602         2301           NA           NA 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V 
        1495          183          887           NA           NA           NA 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF 
          NA         1008          989         2232           NA          942 
TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
         445          917          816          928           NA         1711 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
          NA         2245         3308           NA           NA           NA 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
        2398          334           NA          230          334           44 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
         843         3071          408          386          482          423 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
         406            7            6            6            6            6 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
         400          408          570          608          357          334 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
          NA          303          363           NA           NA          987 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
         729           NA          848           NA           NA            4 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
           1           10         1836           12           37         1553 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        1636          860          935           NA          655          780 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
         180          594          585          447          364          744 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 TCGA-G3-A7M6 TCGA-G3-A7M7 
         621          520          236           NA          366          182 
TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
          NA           NA           NA           NA           NA          631 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
         519          122           NA          360          407          741 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
         387          291          507          559          391          630 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
          NA          135           NA           62          640          579 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
         472          734          455          526          438           NA 
TCGA-UB-A7ME TCGA-UB-A7MF 
         486           NA 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=73,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=103,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 188 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
77 48 50 11 
[1] "table(vv)"
vv
T1 T2 T3 T4 
77 48 50 11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
77 48 50 11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T1 T2 T3 T4 
77 48 50 11 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   34 18
  TP53 WILD-TYPE 65 56
  TP53 MUTATED TP53 WILD-TYPE 
            52            121 
  TP53 MUTATED TP53 WILD-TYPE 
            18             56 
$`TP53 MUTATED`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 
       10.13        27.52        44.42        13.84        22.36         9.50 
TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A1HT 
       14.60        13.45         0.66         0.07         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A11A TCGA-DD-A1EB 
        0.10         0.07         0.10        37.78         2.60        66.31 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EL TCGA-DD-A39Y TCGA-DD-A3A0 TCGA-DD-A3A7 
       45.11         6.02        13.64         5.62        25.81        13.78 
TCGA-DD-A4NQ TCGA-ED-A459 TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-FV-A3I1 
       12.26        13.41         0.20         0.20        13.15         8.12 
TCGA-FV-A3R2 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25U TCGA-G3-A25V 
        6.38         0.33        60.36         0.39        53.79        28.27 
TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M9 
       21.53        19.53        11.97        17.10        12.03         1.84 
TCGA-K7-A5RG TCGA-MI-A75G TCGA-MI-A75I TCGA-QA-A7B7 TCGA-RC-A7SK TCGA-RG-A7D4 
       17.06        18.38        20.71         2.04        15.52        24.13 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7MF 
       17.29        14.40         1.71         7.04 

$`TP53 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       27.91        37.32        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF TCGA-CC-5259 TCGA-CC-5260 
        1.12        69.57         5.03         0.26         0.16         2.86 
TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 
        0.39         3.39         0.13        79.73        83.57        53.33 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
      113.00         7.33         0.46        21.76        51.29        90.71 
TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ 
       79.40        19.79        75.65        12.95        49.15        29.16 
TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
       18.35        21.14        55.69        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 
       17.59        20.12       102.74       107.11         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        30.97        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       73.81       108.76         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20        13.41        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25S 
       23.97        19.10        27.88         0.13         0.03         1.22 
TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       51.06        30.74        14.86        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M7 TCGA-GJ-A6C0 
       14.70        24.46        20.42         7.76         5.98         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
        2.66        37.71        20.75         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75H 
       13.38        24.36        12.72         9.57        16.67        12.85 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-UB-A7MA 
       58.88         4.44        21.01        21.04        19.04        14.96 
TCGA-UB-A7ME 
       15.98 

  TP53 MUTATED TP53 WILD-TYPE 
          0.07           0.03 
  TP53 MUTATED TP53 WILD-TYPE 
         66.31         113.00 
  TP53 MUTATED TP53 WILD-TYPE 
         13.28          19.10 
[1] "0.1 - 66.3 (13.3)"  "0.0 - 113.0 (19.1)"
[1] "hr=" "1.3"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TP53 MUTATED        19       19         0         14          3          0
  TP53 WILD-TYPE      55       24         2         26          4          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TP53 MUTATED          0         0         0
  TP53 WILD-TYPE        2         1         2
D1V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I              19             55
  STAGE II             19             24
  STAGE III             0              2
  STAGE IIIA           14             26
  STAGE IIIB            3              4
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TP53 MUTATED   19 21 17  1
  TP53 WILD-TYPE 58 27 33 10
D1V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1           19             58
  T2           21             27
  T3           17             33
  T4            1             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                cls
clus              0  1
  TP53 MUTATED   33  0
  TP53 WILD-TYPE 86  3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     33    0
  TP53 WILD-TYPE   86    3
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0           33             86
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus             M0 M1 MX
  TP53 MUTATED   43  0 15
  TP53 WILD-TYPE 95  4 31
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           43             95
  M1            0              4
  MX           15             31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   11 47
  TP53 WILD-TYPE 57 73
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     11   47
  TP53 WILD-TYPE   57   73
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           11             57
  MALE             47             73
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TP53 MUTATED                         0                       58
  TP53 WILD-TYPE                       1                      126
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TP53 MUTATED                                  0
  TP53 WILD-TYPE                                3
D1V8, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   58            126
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  TP53 MUTATED    49   3   0   5
  TP53 WILD-TYPE 106   7   1  11
D1V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           49            106
  R1            3              7
  R2            0              1
  RX            5             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TP53 MUTATED                                  1    20
  TP53 WILD-TYPE                                0    32
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED                          10    25
  TP53 WILD-TYPE                         4    88
D1V10, multiclass
                                  clus
vv                                 TP53 MUTATED TP53 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                      20             32
  BLACK OR AFRICAN AMERICAN                  10              4
  WHITE                                      25             88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
                cls
clus               0   1
  TP53 MUTATED     1  53
  TP53 WILD-TYPE   4 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      1   53
  TP53 WILD-TYPE    4  116
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO           53            116
[1] 2 2
[1] FALSE

Clustering(2) Variable = CTNNB1 MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  CTNNB1 MUTATED   29 16
  CTNNB1 WILD-TYPE 70 58
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              45              128 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
              16               58 
$`CTNNB1 MUTATED`
TCGA-BC-A10U TCGA-BC-A5W4 TCGA-BC-A69H TCGA-CC-5262 TCGA-DD-A116 TCGA-DD-A119 
       27.52         9.50        14.60         3.39        53.33         7.33 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       51.29        79.40        75.65        29.16        13.64        21.14 
TCGA-DD-A3A4 TCGA-DD-A4NF TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A73A 
       20.12        30.97        26.83        39.78        56.25        10.98 
TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S 
       10.98         1.45         0.20        13.15        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A4ZQ 
       11.74         0.62         9.96        11.93        23.97         0.39 
TCGA-G3-A25S TCGA-G3-A25Z TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SL 
        1.22        21.53        19.53        19.23        11.97        20.42 
TCGA-G3-A6UC TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-MI-A75C TCGA-MI-A75H TCGA-O8-A75V 
        7.76         4.01         2.14         9.57        12.85         4.44 
TCGA-RG-A7D4 TCGA-UB-A7MC TCGA-UB-A7MD 
       24.13        14.40         1.71 

$`CTNNB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       27.91        37.32        10.13        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 
        0.26        22.36        13.45         0.66         0.07         0.16 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA 
        2.86         0.39         4.24         3.32         0.10         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.10         0.13        79.73        37.78        83.57       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60         0.46        21.76        90.71        66.31        19.79 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X 
       12.95        45.11        49.15         6.02        18.35        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ 
       32.52        73.38        21.70        14.63        30.15        30.51 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
       78.84         9.30         7.56        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A2KB TCGA-ES-A2HS TCGA-ES-A2HT 
        0.20         0.20        13.41        10.98        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       32.45        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.03         0.33        60.36        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK 
       30.74        14.86        25.64         5.92        14.70        24.46 
TCGA-G3-A5SM TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
       17.10        12.03         5.98         1.84         1.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       37.71        20.75        17.06        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75I TCGA-NI-A4U2 TCGA-PD-A5DF 
       12.72        16.67        18.38        20.71        58.88        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MB 
        2.04        21.04        19.04        15.52        14.96        17.29 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            0.20             0.03 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
            79.4            113.0 
  CTNNB1 MUTATED CTNNB1 WILD-TYPE 
          13.640           16.325 
[1] "0.2 - 79.4 (13.6)"  "0.0 - 113.0 (16.3)"
[1] "hr=" "1"  
D2V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  CTNNB1 MUTATED        21       11         0         10          1          2
  CTNNB1 WILD-TYPE      53       32         2         30          6          4
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  CTNNB1 MUTATED          1         1         0
  CTNNB1 WILD-TYPE        1         0         2
D2V3, multiclass
            clus
vv           CTNNB1 MUTATED CTNNB1 WILD-TYPE
  STAGE I                21               53
  STAGE II               11               32
  STAGE III               0                2
  STAGE IIIA             10               30
  STAGE IIIB              1                6
  STAGE IIIC              2                4
  STAGE IV                1                1
  STAGE IVA               1                0
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  CTNNB1 MUTATED   23 12 12  1
  CTNNB1 WILD-TYPE 54 36 38 10
D2V4, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  T1             23               54
  T2             12               36
  T3             12               38
  T4              1               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
                  cls
clus                0  1
  CTNNB1 MUTATED   29  2
  CTNNB1 WILD-TYPE 90  1
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED     29    2
  CTNNB1 WILD-TYPE   90    1
   clus
vv  CTNNB1 MUTATED CTNNB1 WILD-TYPE
  0             29               90
  1              2                1
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  CTNNB1 MUTATED    33   1  15
  CTNNB1 WILD-TYPE 105   3  31
D2V6, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  M0             33              105
  M1              1                3
  MX             15               31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                  cls
clus                0  1
  CTNNB1 MUTATED    6 43
  CTNNB1 WILD-TYPE 62 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      6   43
  CTNNB1 WILD-TYPE   62   77
        clus
vv       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FEMALE              6               62
  MALE               43               77
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  CTNNB1 MUTATED                         0                       49
  CTNNB1 WILD-TYPE                       1                      135
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  CTNNB1 MUTATED                                  0
  CTNNB1 WILD-TYPE                                3
D2V8, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     49              135
  HEPATOCHOLANGIOCARCINOMA (MIXED)              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                R0  R1  R2  RX
  CTNNB1 MUTATED    38   4   1   2
  CTNNB1 WILD-TYPE 117   6   0  14
D2V9, multiclass
    clus
vv   CTNNB1 MUTATED CTNNB1 WILD-TYPE
  R0             38              117
  R1              4                6
  R2              1                0
  RX              2               14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  CTNNB1 MUTATED                                  1    11
  CTNNB1 WILD-TYPE                                0    41
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  CTNNB1 MUTATED                           5    31
  CTNNB1 WILD-TYPE                         9    82
D2V10, multiclass
                                  clus
vv                                 CTNNB1 MUTATED CTNNB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              1                0
  ASIAN                                        11               41
  BLACK OR AFRICAN AMERICAN                     5                9
  WHITE                                        31               82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
                  cls
clus                 0   1
  CTNNB1 MUTATED     1  47
  CTNNB1 WILD-TYPE   4 122
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CTNNB1 MUTATED      1   47
  CTNNB1 WILD-TYPE    4  122
                        clus
vv                       CTNNB1 MUTATED CTNNB1 WILD-TYPE
  HISPANIC OR LATINO                  1                4
  NOT HISPANIC OR LATINO             47              122
[1] 2 2
[1] FALSE

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    7  6
  RB1 WILD-TYPE 92 68
  RB1 MUTATED RB1 WILD-TYPE 
           13           160 
  RB1 MUTATED RB1 WILD-TYPE 
            6            68 
$`RB1 MUTATED`
TCGA-BC-A10W TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A4NE TCGA-DD-A4NJ TCGA-ED-A66Y 
        2.99        79.73        37.78        21.70        30.51         0.23 
TCGA-ED-A7PZ TCGA-G3-A25U TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-RC-A7S9 
        0.20        53.79        14.86        25.64        14.70        21.04 
TCGA-UB-A7MB 
       17.29 

$`RB1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
        3.32         0.10         0.07         0.10         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        14.63        30.15        26.83        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
       13.35         0.20         0.20         0.20        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        28.27        30.74 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK 
       21.53         5.92        19.53        19.23        11.97        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C 
        2.14        11.84        13.38        24.36        12.72         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       16.67        18.38        12.85        20.71        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
       21.01         2.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.40         1.71        15.98         7.04 

  RB1 MUTATED RB1 WILD-TYPE 
         0.20          0.03 
  RB1 MUTATED RB1 WILD-TYPE 
        79.73        113.00 
  RB1 MUTATED RB1 WILD-TYPE 
       21.040        14.795 
[1] "0.2 - 79.7 (21.0)"  "0.0 - 113.0 (14.8)"
[1] "hr=" "1.1"
D3V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  RB1 MUTATED         3        7         0          4          0          0
  RB1 WILD-TYPE      71       36         2         36          7          6
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  RB1 MUTATED          0         0         0
  RB1 WILD-TYPE        2         1         2
D3V3, multiclass
            clus
vv           RB1 MUTATED RB1 WILD-TYPE
  STAGE I              3            71
  STAGE II             7            36
  STAGE III            0             2
  STAGE IIIA           4            36
  STAGE IIIB           0             7
  STAGE IIIC           0             6
  STAGE IV             0             2
  STAGE IVA            0             1
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  RB1 MUTATED    3  7  4  1
  RB1 WILD-TYPE 74 41 46 10
D3V4, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  T1           3            74
  T2           7            41
  T3           4            46
  T4           1            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
               cls
clus              0   1
  RB1 MUTATED    11   0
  RB1 WILD-TYPE 108   3
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED     11    0
  RB1 WILD-TYPE  108    3
   clus
vv  RB1 MUTATED RB1 WILD-TYPE
  0          11           108
  1           0             3
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  RB1 MUTATED    13   0   2
  RB1 WILD-TYPE 125   4  44
D3V6, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  M0          13           125
  M1           0             4
  MX           2            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
               cls
clus              0   1
  RB1 MUTATED     7   8
  RB1 WILD-TYPE  61 112
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      7    8
  RB1 WILD-TYPE   61  112
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           7            61
  MALE             8           112
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  RB1 MUTATED                         0                       15
  RB1 WILD-TYPE                       1                      169
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  RB1 MUTATED                                  0
  RB1 WILD-TYPE                                3
D3V8, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  15           169
  HEPATOCHOLANGIOCARCINOMA (MIXED)           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             R0  R1  R2  RX
  RB1 MUTATED    14   1   0   0
  RB1 WILD-TYPE 141   9   1  16
D3V9, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  R0          14           141
  R1           1             9
  R2           0             1
  RX           0            16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  RB1 MUTATED                                  0    10
  RB1 WILD-TYPE                                1    42
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED                           1     4
  RB1 WILD-TYPE                        13   109
D3V10, multiclass
                                  clus
vv                                 RB1 MUTATED RB1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           0             1
  ASIAN                                     10            42
  BLACK OR AFRICAN AMERICAN                  1            13
  WHITE                                      4           109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
               cls
clus              0   1
  RB1 MUTATED     1  14
  RB1 WILD-TYPE   4 155
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      1   14
  RB1 WILD-TYPE    4  155
                        clus
vv                       RB1 MUTATED RB1 WILD-TYPE
  HISPANIC OR LATINO               1             4
  NOT HISPANIC OR LATINO          14           155
[1] 2 2
[1] FALSE

Clustering(4) Variable = AXIN1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  AXIN1 MUTATED    1  5
  AXIN1 WILD-TYPE 98 69
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              6             167 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
              5              69 
$`AXIN1 MUTATED`
TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A39Z TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A3R2 
        0.46        49.15        19.76        22.85        32.45         6.38 

$`AXIN1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        75.65        12.95        45.11         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ 
       21.70        30.97        14.63        30.15        26.83        30.51 
TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ 
       39.78        56.25        29.56        73.81       108.76        12.26 
TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
        0.30        80.75        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20        13.15        13.41        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
       11.74        10.98         0.62         9.96        11.93        14.40 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-FV-A495 
       23.97        19.10        27.88         8.12         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.33        60.36         0.39         1.22        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       28.27        30.74        14.86        21.53        25.64         5.92 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       19.53        19.23        14.70        11.97        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       17.10         7.76        12.03         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36        12.72         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        12.85        20.71        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.29        14.40         1.71        15.98         7.04 

  AXIN1 MUTATED AXIN1 WILD-TYPE 
           0.46            0.03 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
          49.15          113.00 
  AXIN1 MUTATED AXIN1 WILD-TYPE 
         21.305          14.960 
[1] "0.5 - 49.1 (21.3)"  "0.0 - 113.0 (15.0)"
[1] "hr=" "2.1"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AXIN1 MUTATED         3        2         1          1          1          0
  AXIN1 WILD-TYPE      71       41         1         39          6          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  AXIN1 MUTATED          1         0         0
  AXIN1 WILD-TYPE        1         1         2
D4V3, multiclass
            clus
vv           AXIN1 MUTATED AXIN1 WILD-TYPE
  STAGE I                3              71
  STAGE II               2              41
  STAGE III              1               1
  STAGE IIIA             1              39
  STAGE IIIB             1               6
  STAGE IIIC             0               6
  STAGE IV               1               1
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  AXIN1 MUTATED    3  3  2  1
  AXIN1 WILD-TYPE 74 45 48 10
D4V4, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  T1             3              74
  T2             3              45
  T3             2              48
  T4             1              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V5, binary
                 cls
clus                0   1
  AXIN1 MUTATED     6   0
  AXIN1 WILD-TYPE 113   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      6    0
  AXIN1 WILD-TYPE  113    3
   clus
vv  AXIN1 MUTATED AXIN1 WILD-TYPE
  0             6             113
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  AXIN1 MUTATED     6   1   2
  AXIN1 WILD-TYPE 132   3  44
D4V6, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  M0             6             132
  M1             1               3
  MX             2              44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                 cls
clus                0   1
  AXIN1 MUTATED     3   6
  AXIN1 WILD-TYPE  65 114
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      3    6
  AXIN1 WILD-TYPE   65  114
        clus
vv       AXIN1 MUTATED AXIN1 WILD-TYPE
  FEMALE             3              65
  MALE               6             114
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  AXIN1 MUTATED                         0                        9
  AXIN1 WILD-TYPE                       1                      175
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  AXIN1 MUTATED                                  0
  AXIN1 WILD-TYPE                                3
D4V8, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             175
  HEPATOCHOLANGIOCARCINOMA (MIXED)             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               R0  R1  R2  RX
  AXIN1 MUTATED     7   0   0   2
  AXIN1 WILD-TYPE 148  10   1  14
D4V9, multiclass
    clus
vv   AXIN1 MUTATED AXIN1 WILD-TYPE
  R0             7             148
  R1             0              10
  R2             0               1
  RX             2              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AXIN1 MUTATED                                  0     2
  AXIN1 WILD-TYPE                                1    50
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  AXIN1 MUTATED                           0     6
  AXIN1 WILD-TYPE                        14   107
D4V10, multiclass
                                  clus
vv                                 AXIN1 MUTATED AXIN1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        2              50
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        6             107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
                 cls
clus                0   1
  AXIN1 MUTATED     1   7
  AXIN1 WILD-TYPE   4 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  AXIN1 MUTATED      1    7
  AXIN1 WILD-TYPE    4  162
                        clus
vv                       AXIN1 MUTATED AXIN1 WILD-TYPE
  HISPANIC OR LATINO                 1               4
  NOT HISPANIC OR LATINO             7             162
[1] 2 2
[1] FALSE

Clustering(5) Variable = BAP1 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  BAP1 MUTATED    6  4
  BAP1 WILD-TYPE 93 70
  BAP1 MUTATED BAP1 WILD-TYPE 
            10            163 
  BAP1 MUTATED BAP1 WILD-TYPE 
             4             70 
$`BAP1 MUTATED`
TCGA-BC-A10Q TCGA-CC-5260 TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A3A9 TCGA-DD-A4NA 
       37.32         2.86       113.00        12.95        30.61        33.14 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A7PX TCGA-G3-A25T 
      100.96        12.69         0.20        51.06 

$`BAP1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       27.91        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT 
        0.07         0.16         0.39         3.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL 
       45.11        49.15         6.02        29.16        18.35        13.64 
TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       21.14        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
        0.36        32.52        73.38        21.70        30.97        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PY 
       13.41        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S 
        0.20         0.20        13.15        13.41        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
       11.74        10.98         0.62         9.96        11.93        22.85 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        1.22        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.84         1.02         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK 
        4.44        21.01         2.04        21.04        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       24.13        14.96        17.29        14.40         1.71        15.98 
TCGA-UB-A7MF 
        7.04 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.20           0.03 
  BAP1 MUTATED BAP1 WILD-TYPE 
        113.00         108.76 
  BAP1 MUTATED BAP1 WILD-TYPE 
        31.875         14.960 
[1] "0.2 - 113.0 (31.9)" "0.0 - 108.8 (15.0)"
[1] "hr=" "1.9"
D5V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  BAP1 MUTATED         2        3         0          1          0          2
  BAP1 WILD-TYPE      72       40         2         39          7          4
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  BAP1 MUTATED          0         0         1
  BAP1 WILD-TYPE        2         1         1
D5V3, multiclass
            clus
vv           BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I               2             72
  STAGE II              3             40
  STAGE III             0              2
  STAGE IIIA            1             39
  STAGE IIIB            0              7
  STAGE IIIC            2              4
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  BAP1 MUTATED    2  5  1  2
  BAP1 WILD-TYPE 75 43 49  9
D5V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            2             75
  T2            5             43
  T3            1             49
  T4            2              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
                cls
clus               0   1
  BAP1 MUTATED     7   1
  BAP1 WILD-TYPE 112   2
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      7    1
  BAP1 WILD-TYPE  112    2
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0            7            112
  1            1              2
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  BAP1 MUTATED     8   1   1
  BAP1 WILD-TYPE 130   3  45
D5V6, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  M0            8            130
  M1            1              3
  MX            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                cls
clus               0   1
  BAP1 MUTATED     9   1
  BAP1 WILD-TYPE  59 119
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      9    1
  BAP1 WILD-TYPE   59  119
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE            9             59
  MALE              1            119
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  BAP1 MUTATED                         0                       10
  BAP1 WILD-TYPE                       1                      174
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  BAP1 MUTATED                                  0
  BAP1 WILD-TYPE                                3
D5V8, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   10            174
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  BAP1 MUTATED     8   1   0   1
  BAP1 WILD-TYPE 147   9   1  15
D5V9, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  R0            8            147
  R1            1              9
  R2            0              1
  RX            1             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  BAP1 MUTATED                                  0     3
  BAP1 WILD-TYPE                                1    49
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED                           0     7
  BAP1 WILD-TYPE                        14   106
D5V10, multiclass
                                  clus
vv                                 BAP1 MUTATED BAP1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       3             49
  BLACK OR AFRICAN AMERICAN                   0             14
  WHITE                                       7            106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
                cls
clus               0   1
  BAP1 MUTATED     0  10
  BAP1 WILD-TYPE   5 159
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      0   10
  BAP1 WILD-TYPE    5  159
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           10            159
[1] 2 2
[1] FALSE

Clustering(6) Variable = TSC2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  TSC2 MUTATED    3  5
  TSC2 WILD-TYPE 96 69
  TSC2 MUTATED TSC2 WILD-TYPE 
             8            165 
  TSC2 MUTATED TSC2 WILD-TYPE 
             5             69 
$`TSC2 MUTATED`
TCGA-BC-A3KF TCGA-DD-A114 TCGA-DD-A39Z TCGA-DD-A3A6 TCGA-DD-A4NH TCGA-DD-A4NQ 
        0.26        37.78        19.76       107.11        30.15        12.26 
TCGA-G3-A25S TCGA-MI-A75I 
        1.22        20.71 

$`TSC2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
       13.84        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A3A0 
       18.35        13.64        21.14        55.69         5.62        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A7 
        7.66        70.06        17.59        20.12       102.74        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        14.63        26.83        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       29.56        73.81       108.76         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
      100.96        13.41        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.41        18.74        19.99        11.74        10.98         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ 
        9.96        11.93        22.85        14.40        32.45        23.97 
TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 
       19.10        27.88         8.12         6.38         0.13         0.03 
TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.33        60.36         0.39        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       30.74        14.86        21.53        25.64         5.92        19.53 
TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM 
       19.23        14.70        11.97        24.46        20.42        17.10 
TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ 
        7.76        12.03         5.98         1.84         1.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 
       37.71        20.75        17.06         4.01         2.14        11.84 
TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G 
       13.38        24.36        12.72         9.57        16.67        18.38 
TCGA-MI-A75H TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       12.85        58.88         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC 
       19.04        15.52        24.13        14.96        17.29        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        1.71        15.98         7.04 

  TSC2 MUTATED TSC2 WILD-TYPE 
          0.26           0.03 
  TSC2 MUTATED TSC2 WILD-TYPE 
        107.11         113.00 
  TSC2 MUTATED TSC2 WILD-TYPE 
        20.235         14.960 
[1] "0.3 - 107.1 (20.2)" "0.0 - 113.0 (15.0)"
[1] "hr=" "1.1"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  TSC2 MUTATED         2        5         0          0          1          0
  TSC2 WILD-TYPE      72       38         2         40          6          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  TSC2 MUTATED          0         0         0
  TSC2 WILD-TYPE        2         1         2
D6V3, multiclass
            clus
vv           TSC2 MUTATED TSC2 WILD-TYPE
  STAGE I               2             72
  STAGE II              5             38
  STAGE III             0              2
  STAGE IIIA            0             40
  STAGE IIIB            1              6
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  TSC2 MUTATED    2  6  1  0
  TSC2 WILD-TYPE 75 42 49 11
D6V4, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  T1            2             75
  T2            6             42
  T3            1             49
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
                cls
clus               0   1
  TSC2 MUTATED     5   0
  TSC2 WILD-TYPE 114   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      5    0
  TSC2 WILD-TYPE  114    3
   clus
vv  TSC2 MUTATED TSC2 WILD-TYPE
  0            5            114
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  TSC2 MUTATED     8   0   1
  TSC2 WILD-TYPE 130   4  45
D6V6, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  M0            8            130
  M1            0              4
  MX            1             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                cls
clus               0   1
  TSC2 MUTATED     4   5
  TSC2 WILD-TYPE  64 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      4    5
  TSC2 WILD-TYPE   64  115
        clus
vv       TSC2 MUTATED TSC2 WILD-TYPE
  FEMALE            4             64
  MALE              5            115
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  TSC2 MUTATED                         0                        9
  TSC2 WILD-TYPE                       1                      175
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  TSC2 MUTATED                                  0
  TSC2 WILD-TYPE                                3
D6V8, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    9            175
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  TSC2 MUTATED     8   1   0   0
  TSC2 WILD-TYPE 147   9   1  16
D6V9, multiclass
    clus
vv   TSC2 MUTATED TSC2 WILD-TYPE
  R0            8            147
  R1            1              9
  R2            0              1
  RX            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  TSC2 MUTATED                                  0     1
  TSC2 WILD-TYPE                                1    51
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  TSC2 MUTATED                           2     5
  TSC2 WILD-TYPE                        12   108
D6V10, multiclass
                                  clus
vv                                 TSC2 MUTATED TSC2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             51
  BLACK OR AFRICAN AMERICAN                   2             12
  WHITE                                       5            108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
                cls
clus               0   1
  TSC2 MUTATED     1   6
  TSC2 WILD-TYPE   4 163
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC2 MUTATED      1    6
  TSC2 WILD-TYPE    4  163
                        clus
vv                       TSC2 MUTATED TSC2 WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            6            163
[1] 2 2
[1] FALSE

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    5  7
  ARID1A WILD-TYPE 94 67
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              161 
  ARID1A MUTATED ARID1A WILD-TYPE 
               7               67 
$`ARID1A MUTATED`
TCGA-CC-5258 TCGA-CC-5262 TCGA-DD-A1EH TCGA-DD-A39V TCGA-DD-A4NR TCGA-EP-A2KB 
        0.07         3.39        49.15        21.14         0.30        10.98 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-UB-A7MD TCGA-UB-A7ME 
       14.40        32.45        24.36        12.72         1.71        15.98 

$`ARID1A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT 
        0.66         0.16         2.86         0.39         4.24         3.32 
TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        0.10         0.07         0.10         0.13        79.73        37.78 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       75.65        12.95        45.11         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 
       13.64        55.69         5.62        19.76        25.81         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        14.63        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS 
       56.25        29.56        73.81       108.76        12.26        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       13.15        13.41        18.74        19.99        11.74         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
        9.96        11.93        22.85        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97        24.46        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.03         5.98         1.84         1.02         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK 
        4.44        21.01         2.04        21.04        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF 
       24.13        14.96        17.29        14.40         7.04 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.07             0.03 
  ARID1A MUTATED ARID1A WILD-TYPE 
           49.15           113.00 
  ARID1A MUTATED ARID1A WILD-TYPE 
           13.56            15.85 
[1] "0.1 - 49.1 (13.6)"  "0.0 - 113.0 (15.8)"
[1] "hr=" "2.1"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ARID1A MUTATED         7        4         1          1          0          1
  ARID1A WILD-TYPE      67       39         1         39          7          5
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  ARID1A MUTATED          0         0         0
  ARID1A WILD-TYPE        2         1         2
D7V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 7               67
  STAGE II                4               39
  STAGE III               1                1
  STAGE IIIA              1               39
  STAGE IIIB              0                7
  STAGE IIIC              1                5
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  ARID1A MUTATED    7  4  2  1
  ARID1A WILD-TYPE 70 44 48 10
D7V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              7               70
  T2              4               44
  T3              2               48
  T4              1               10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED     8   0
  ARID1A WILD-TYPE 111   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      8    0
  ARID1A WILD-TYPE  111    3
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              8              111
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  ARID1A MUTATED     9   0   5
  ARID1A WILD-TYPE 129   4  41
D7V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0              9              129
  M1              0                4
  MX              5               41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     5   9
  ARID1A WILD-TYPE  63 111
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    9
  ARID1A WILD-TYPE   63  111
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              5               63
  MALE                9              111
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ARID1A MUTATED                         0                       14
  ARID1A WILD-TYPE                       1                      170
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  ARID1A MUTATED                                  0
  ARID1A WILD-TYPE                                3
D7V8, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                     14              170
  HEPATOCHOLANGIOCARCINOMA (MIXED)              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                R0  R1  R2  RX
  ARID1A MUTATED    10   0   0   3
  ARID1A WILD-TYPE 145  10   1  13
D7V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0             10              145
  R1              0               10
  R2              0                1
  RX              3               13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ARID1A MUTATED                                  0     4
  ARID1A WILD-TYPE                                1    48
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED                           2     7
  ARID1A WILD-TYPE                        12   106
D7V10, multiclass
                                  clus
vv                                 ARID1A MUTATED ARID1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         4               48
  BLACK OR AFRICAN AMERICAN                     2               12
  WHITE                                         7              106
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
                  cls
clus                 0   1
  ARID1A MUTATED     0  13
  ARID1A WILD-TYPE   5 156
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      0   13
  ARID1A WILD-TYPE    5  156
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO             13              156
[1] 2 2
[1] FALSE

Clustering(8) Variable = IL6ST MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  IL6ST MUTATED    6  0
  IL6ST WILD-TYPE 93 74
  IL6ST MUTATED IL6ST WILD-TYPE 
              6             167 
  IL6ST MUTATED IL6ST WILD-TYPE 
              0              74 
$`IL6ST MUTATED`
TCGA-DD-A118 TCGA-DD-A1ED TCGA-DD-A4NL TCGA-DD-A4NP TCGA-ED-A459 TCGA-G3-A3CK 
      113.00        75.65        56.25       108.76        13.41        19.23 

$`IL6ST WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.79        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        30.97        14.63        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A4NR 
       30.51        39.78        29.56        73.81        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
        1.45        27.72       100.96        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
        5.92        19.53        14.70        11.97        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 
       17.10         7.76        12.03         5.98         1.84         1.02 
TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 
        2.66        37.71        20.75        17.06         4.01         2.14 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36        12.72         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        12.85        20.71        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.29        14.40         1.71        15.98         7.04 

  IL6ST MUTATED IL6ST WILD-TYPE 
          13.41            0.03 
  IL6ST MUTATED IL6ST WILD-TYPE 
         113.00          107.11 
  IL6ST MUTATED IL6ST WILD-TYPE 
          65.95           14.86 
[1] "13.4 - 113.0 (66.0)" "0.0 - 107.1 (14.9)" 
[1] "hr="   "1e+08"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  IL6ST MUTATED         4        2         0          1          0          0
  IL6ST WILD-TYPE      70       41         2         39          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  IL6ST MUTATED          0         0         0
  IL6ST WILD-TYPE        2         1         2
D8V3, multiclass
            clus
vv           IL6ST MUTATED IL6ST WILD-TYPE
  STAGE I                4              70
  STAGE II               2              41
  STAGE III              0               2
  STAGE IIIA             1              39
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  IL6ST MUTATED    4  2  1  0
  IL6ST WILD-TYPE 73 46 49 11
D8V4, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  T1             4              73
  T2             2              46
  T3             1              49
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
                 cls
clus                0   1
  IL6ST MUTATED     7   0
  IL6ST WILD-TYPE 112   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      7    0
  IL6ST WILD-TYPE  112    3
   clus
vv  IL6ST MUTATED IL6ST WILD-TYPE
  0             7             112
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  IL6ST MUTATED     7   0   0
  IL6ST WILD-TYPE 131   4  46
D8V6, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  M0             7             131
  M1             0               4
  MX             0              46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                 cls
clus                0   1
  IL6ST MUTATED     2   5
  IL6ST WILD-TYPE  66 115
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      2    5
  IL6ST WILD-TYPE   66  115
        clus
vv       IL6ST MUTATED IL6ST WILD-TYPE
  FEMALE             2              66
  MALE               5             115
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  IL6ST MUTATED                         0                        7
  IL6ST WILD-TYPE                       1                      177
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  IL6ST MUTATED                                  0
  IL6ST WILD-TYPE                                3
D8V8, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     7             177
  HEPATOCHOLANGIOCARCINOMA (MIXED)             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               R0  R1  R2  RX
  IL6ST MUTATED     6   0   0   1
  IL6ST WILD-TYPE 149  10   1  15
D8V9, multiclass
    clus
vv   IL6ST MUTATED IL6ST WILD-TYPE
  R0             6             149
  R1             0              10
  R2             0               1
  RX             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  IL6ST MUTATED                                  0     3
  IL6ST WILD-TYPE                                1    49
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  IL6ST MUTATED                           0     4
  IL6ST WILD-TYPE                        14   109
D8V10, multiclass
                                  clus
vv                                 IL6ST MUTATED IL6ST WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3              49
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        4             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
                 cls
clus                0   1
  IL6ST MUTATED     0   7
  IL6ST WILD-TYPE   5 162
[1] "tbl2"
                 cls
clus              [,1] [,2]
  IL6ST MUTATED      0    7
  IL6ST WILD-TYPE    5  162
                        clus
vv                       IL6ST MUTATED IL6ST WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             7             162
[1] 2 2
[1] FALSE

Clustering(9) Variable = ALB MUTATION ANALYSIS
D9V1, survival
               sevent
clus2            0  1
  ALB MUTATED   11  6
  ALB WILD-TYPE 88 68
  ALB MUTATED ALB WILD-TYPE 
           17           156 
  ALB MUTATED ALB WILD-TYPE 
            6            68 
$`ALB MUTATED`
TCGA-BC-4073 TCGA-DD-A1E9 TCGA-DD-A39X TCGA-DD-A4NI TCGA-DD-A4NK TCGA-EP-A26S 
       27.91        90.71        55.69        26.83        39.78        19.99 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-G3-A25S TCGA-G3-A3CJ 
        0.62         9.96        22.85        23.97         1.22        19.53 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-K7-A6G5 TCGA-MI-A75E TCGA-MI-A75G 
       11.97        24.46         4.01        16.67        18.38 

$`ALB WILD-TYPE`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       37.32        10.13        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        21.76        51.29        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       18.35        13.64        21.14         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NL 
       21.70        30.97        14.63        30.15        30.51        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK 
       13.15        13.41        18.74        11.74        10.98        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       14.40        32.45        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25T 
        0.13         0.03         0.33        60.36         0.39        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
        5.92        19.23        14.70        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.03         5.98         1.84         1.02         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       20.75        17.06         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V 
       12.72         9.57        12.85        20.71        58.88         4.44 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
       21.01         2.04        21.04        19.04        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 

  ALB MUTATED ALB WILD-TYPE 
         0.62          0.03 
  ALB MUTATED ALB WILD-TYPE 
        90.71        113.00 
  ALB MUTATED ALB WILD-TYPE 
       19.990        14.665 
[1] "0.6 - 90.7 (20.0)"  "0.0 - 113.0 (14.7)"
[1] "hr=" "1.3"
D9V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  ALB MUTATED        10        3         0          2          1          1
  ALB WILD-TYPE      64       40         2         38          6          5
               vv
clus            STAGE IV STAGE IVA STAGE IVB
  ALB MUTATED          0         1         0
  ALB WILD-TYPE        2         0         2
D9V3, multiclass
            clus
vv           ALB MUTATED ALB WILD-TYPE
  STAGE I             10            64
  STAGE II             3            40
  STAGE III            0             2
  STAGE IIIA           2            38
  STAGE IIIB           1             6
  STAGE IIIC           1             5
  STAGE IV             0             2
  STAGE IVA            1             0
  STAGE IVB            0             2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            T1 T2 T3 T4
  ALB MUTATED   11  3  2  2
  ALB WILD-TYPE 66 45 48  9
D9V4, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  T1          11            66
  T2           3            45
  T3           2            48
  T4           2             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V5, binary
               cls
clus              0   1
  ALB MUTATED    10   1
  ALB WILD-TYPE 109   2
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED     10    1
  ALB WILD-TYPE  109    2
   clus
vv  ALB MUTATED ALB WILD-TYPE
  0          10           109
  1           1             2
[1] 2 2
[1] FALSE
               vv
clus             M0  M1  MX
  ALB MUTATED    11   0   7
  ALB WILD-TYPE 127   4  39
D9V6, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  M0          11           127
  M1           0             4
  MX           7            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
               cls
clus              0   1
  ALB MUTATED     2  16
  ALB WILD-TYPE  66 104
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      2   16
  ALB WILD-TYPE   66  104
        clus
vv       ALB MUTATED ALB WILD-TYPE
  FEMALE           2            66
  MALE            16           104
[1] 2 2
[1] FALSE
               vv
clus            FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  ALB MUTATED                         0                       18
  ALB WILD-TYPE                       1                      166
               vv
clus            HEPATOCHOLANGIOCARCINOMA (MIXED)
  ALB MUTATED                                  0
  ALB WILD-TYPE                                3
D9V8, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                    0             1
  HEPATOCELLULAR CARCINOMA                  18           166
  HEPATOCHOLANGIOCARCINOMA (MIXED)           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             R0  R1  R2  RX
  ALB MUTATED    13   2   0   1
  ALB WILD-TYPE 142   8   1  15
D9V9, multiclass
    clus
vv   ALB MUTATED ALB WILD-TYPE
  R0          13           142
  R1           2             8
  R2           0             1
  RX           1            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  ALB MUTATED                                  1     1
  ALB WILD-TYPE                                0    51
               vv
clus            BLACK OR AFRICAN AMERICAN WHITE
  ALB MUTATED                           1    15
  ALB WILD-TYPE                        13    98
D9V10, multiclass
                                  clus
vv                                 ALB MUTATED ALB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE           1             0
  ASIAN                                      1            51
  BLACK OR AFRICAN AMERICAN                  1            13
  WHITE                                     15            98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
               cls
clus              0   1
  ALB MUTATED     0  18
  ALB WILD-TYPE   5 151
[1] "tbl2"
               cls
clus            [,1] [,2]
  ALB MUTATED      0   18
  ALB WILD-TYPE    5  151
                        clus
vv                       ALB MUTATED ALB WILD-TYPE
  HISPANIC OR LATINO               0             5
  NOT HISPANIC OR LATINO          18           151
[1] 2 2
[1] FALSE

Clustering(10) Variable = HNF1A MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  HNF1A MUTATED    4  2
  HNF1A WILD-TYPE 95 72
  HNF1A MUTATED HNF1A WILD-TYPE 
              6             167 
  HNF1A MUTATED HNF1A WILD-TYPE 
              2              72 
$`HNF1A MUTATED`
TCGA-CC-A3M9 TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A3A2 TCGA-DD-A73C TCGA-NI-A4U2 
        0.10        21.76        66.31        70.06         7.56        58.88 

$`HNF1A WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        4.24         3.32         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
        0.46        51.29        90.71        79.40        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       13.64        21.14        55.69         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
        7.66        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        14.63        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-A73E 
       80.75        78.84        10.98         9.30        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 
       27.72       100.96        13.41        12.69        15.85        13.91 
TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO 
       13.35         0.23         0.20         0.20         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       13.15        13.41        18.74        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       53.79        28.27        30.74        14.86        21.53        25.64 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK 
        5.92        19.53        19.23        14.70        11.97        24.46 
TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 
       20.42        17.10         7.76        12.03         5.98         1.84 
TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.02         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C 
        2.14        11.84        13.38        24.36        12.72         9.57 
TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        18.38        12.85        20.71         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.29        14.40         1.71        15.98         7.04 

  HNF1A MUTATED HNF1A WILD-TYPE 
           0.10            0.03 
  HNF1A MUTATED HNF1A WILD-TYPE 
          70.06          113.00 
  HNF1A MUTATED HNF1A WILD-TYPE 
          40.32           14.96 
[1] "0.1 - 70.1 (40.3)"  "0.0 - 113.0 (15.0)"
[1] "hr=" "2"  
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  HNF1A MUTATED         3        0         0          3          0          0
  HNF1A WILD-TYPE      71       43         2         37          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  HNF1A MUTATED          0         0         0
  HNF1A WILD-TYPE        2         1         2
D10V3, multiclass
            clus
vv           HNF1A MUTATED HNF1A WILD-TYPE
  STAGE I                3              71
  STAGE II               0              43
  STAGE III              0               2
  STAGE IIIA             3              37
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  HNF1A MUTATED    3  0  3  0
  HNF1A WILD-TYPE 74 48 47 11
D10V4, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  T1             3              74
  T2             0              48
  T3             3              47
  T4             0              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V5, binary
                 cls
clus                0   1
  HNF1A MUTATED     5   0
  HNF1A WILD-TYPE 114   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      5    0
  HNF1A WILD-TYPE  114    3
   clus
vv  HNF1A MUTATED HNF1A WILD-TYPE
  0             5             114
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  HNF1A MUTATED     5   0   1
  HNF1A WILD-TYPE 133   4  45
D10V6, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  M0             5             133
  M1             0               4
  MX             1              45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                 cls
clus                0   1
  HNF1A MUTATED     3   3
  HNF1A WILD-TYPE  65 117
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      3    3
  HNF1A WILD-TYPE   65  117
        clus
vv       HNF1A MUTATED HNF1A WILD-TYPE
  FEMALE             3              65
  MALE               3             117
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HNF1A MUTATED                         0                        6
  HNF1A WILD-TYPE                       1                      178
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  HNF1A MUTATED                                  0
  HNF1A WILD-TYPE                                3
D10V8, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     6             178
  HEPATOCHOLANGIOCARCINOMA (MIXED)             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               R0  R1  R2  RX
  HNF1A MUTATED     5   0   0   1
  HNF1A WILD-TYPE 150  10   1  15
D10V9, multiclass
    clus
vv   HNF1A MUTATED HNF1A WILD-TYPE
  R0             5             150
  R1             0              10
  R2             0               1
  RX             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HNF1A MUTATED                                  0     1
  HNF1A WILD-TYPE                                1    51
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  HNF1A MUTATED                           0     4
  HNF1A WILD-TYPE                        14   109
D10V10, multiclass
                                  clus
vv                                 HNF1A MUTATED HNF1A WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        1              51
  BLACK OR AFRICAN AMERICAN                    0              14
  WHITE                                        4             109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
                 cls
clus                0   1
  HNF1A MUTATED     0   5
  HNF1A WILD-TYPE   5 164
[1] "tbl2"
                 cls
clus              [,1] [,2]
  HNF1A MUTATED      0    5
  HNF1A WILD-TYPE    5  164
                        clus
vv                       HNF1A MUTATED HNF1A WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             5             164
[1] 2 2
[1] FALSE

Clustering(11) Variable = APOB MUTATION ANALYSIS
D11V1, survival
                sevent
clus2             0  1
  APOB MUTATED   11  9
  APOB WILD-TYPE 88 65
  APOB MUTATED APOB WILD-TYPE 
            20            153 
  APOB MUTATED APOB WILD-TYPE 
             9             65 
$`APOB MUTATED`
TCGA-BC-A10Z TCGA-CC-5258 TCGA-CC-5259 TCGA-DD-A1EA TCGA-DD-A1EK TCGA-DD-A3A5 
        1.12         0.07         0.16        79.40        18.35       102.74 
TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NS TCGA-ED-A7XP TCGA-EP-A12J TCGA-G3-A25W 
       13.78        14.63        80.75        13.15        18.74        30.74 
TCGA-G3-A25Y TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A7M6 TCGA-HP-A5MZ TCGA-KR-A7K0 
       14.86         5.92        19.53        12.03         2.66         2.14 
TCGA-RC-A7S9 TCGA-UB-A7MB 
       21.04        17.29 

$`APOB WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34        69.57         5.03        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 
        2.86         0.39         3.39         4.24         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF 
       51.29        90.71        66.31        19.79        75.65        12.95 
TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39V 
       45.11        49.15         6.02        29.16        13.64        21.14 
TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 
       55.69         5.62        19.76        25.81         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
       17.59        20.12       107.11         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NH TCGA-DD-A4NI 
       32.52        73.38        21.70        30.97        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
       12.26         0.30        78.84        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI 
       10.98         1.45        27.72       100.96        13.41        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       15.85        13.91        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        13.41        19.99        11.74        10.98 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
        0.62         9.96        11.93        22.85        14.40        32.45 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
       23.97        19.10        27.88         8.12         6.38         0.13 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
        0.03         0.33        60.36         0.39         1.22        51.06 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CK TCGA-G3-A5SI 
       53.79        28.27        21.53        25.64        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M7 
       11.97        24.46        20.42        17.10         7.76         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        1.84         1.02        37.71        20.75        17.06         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E 
       11.84        13.38        24.36        12.72         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        12.85        20.71        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC 
        2.04        19.04        15.52        24.13        14.96        14.40 
TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
        1.71        15.98         7.04 

  APOB MUTATED APOB WILD-TYPE 
          0.07           0.03 
  APOB MUTATED APOB WILD-TYPE 
        102.74         113.00 
  APOB MUTATED APOB WILD-TYPE 
        14.745         15.850 
[1] "0.1 - 102.7 (14.7)" "0.0 - 113.0 (15.8)"
[1] "hr=" "1.1"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  APOB MUTATED        10        6         1          2          2          1
  APOB WILD-TYPE      64       37         1         38          5          5
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  APOB MUTATED          0         0         1
  APOB WILD-TYPE        2         1         1
D11V3, multiclass
            clus
vv           APOB MUTATED APOB WILD-TYPE
  STAGE I              10             64
  STAGE II              6             37
  STAGE III             1              1
  STAGE IIIA            2             38
  STAGE IIIB            2              5
  STAGE IIIC            1              5
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             1              1
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  APOB MUTATED   10  6  5  2
  APOB WILD-TYPE 67 42 45  9
D11V4, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  T1           10             67
  T2            6             42
  T3            5             45
  T4            2              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V5, binary
                cls
clus               0   1
  APOB MUTATED    17   0
  APOB WILD-TYPE 102   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     17    0
  APOB WILD-TYPE  102    3
   clus
vv  APOB MUTATED APOB WILD-TYPE
  0           17            102
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  APOB MUTATED    17   1   5
  APOB WILD-TYPE 121   3  41
D11V6, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  M0           17            121
  M1            1              3
  MX            5             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                cls
clus               0   1
  APOB MUTATED    10  13
  APOB WILD-TYPE  58 107
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED     10   13
  APOB WILD-TYPE   58  107
        clus
vv       APOB MUTATED APOB WILD-TYPE
  FEMALE           10             58
  MALE             13            107
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  APOB MUTATED                         0                       23
  APOB WILD-TYPE                       1                      161
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  APOB MUTATED                                  0
  APOB WILD-TYPE                                3
D11V8, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                   23            161
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  APOB MUTATED    21   0   0   2
  APOB WILD-TYPE 134  10   1  14
D11V9, multiclass
    clus
vv   APOB MUTATED APOB WILD-TYPE
  R0           21            134
  R1            0             10
  R2            0              1
  RX            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  APOB MUTATED                                  1     9
  APOB WILD-TYPE                                0    43
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  APOB MUTATED                           1    10
  APOB WILD-TYPE                        13   103
D11V10, multiclass
                                  clus
vv                                 APOB MUTATED APOB WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            1              0
  ASIAN                                       9             43
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                      10            103
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
                cls
clus               0   1
  APOB MUTATED     0  20
  APOB WILD-TYPE   5 149
[1] "tbl2"
                cls
clus             [,1] [,2]
  APOB MUTATED      0   20
  APOB WILD-TYPE    5  149
                        clus
vv                       APOB MUTATED APOB WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO           20            149
[1] 2 2
[1] FALSE

Clustering(12) Variable = EEF1A1 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2               0  1
  EEF1A1 MUTATED    2  3
  EEF1A1 WILD-TYPE 97 71
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               5              168 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
               3               71 
$`EEF1A1 MUTATED`
TCGA-DD-A11B TCGA-G3-A25V TCGA-G3-A5SM TCGA-KR-A7K0 TCGA-UB-A7MD 
        0.46        28.27        17.10         2.14         1.71 

$`EEF1A1 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        30.97        14.63        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W 
       60.36         0.39         1.22        51.06        53.79        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-A7M6 
       14.70        11.97        24.46        20.42         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        5.98         1.84         1.02         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
       17.06         4.01        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK 
        4.44        21.01         2.04        21.04        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF 
       24.13        14.96        17.29        14.40        15.98         7.04 

  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
            0.46             0.03 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           28.27           113.00 
  EEF1A1 MUTATED EEF1A1 WILD-TYPE 
           2.140           15.685 
[1] "0.5 - 28.3 (2.1)"   "0.0 - 113.0 (15.7)"
[1] "hr=" "3"  
D12V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  EEF1A1 MUTATED         4        1         0          0          0          0
  EEF1A1 WILD-TYPE      70       42         2         40          7          6
                  vv
clus               STAGE IV STAGE IVA STAGE IVB
  EEF1A1 MUTATED          0         0         0
  EEF1A1 WILD-TYPE        2         1         2
D12V3, multiclass
            clus
vv           EEF1A1 MUTATED EEF1A1 WILD-TYPE
  STAGE I                 4               70
  STAGE II                1               42
  STAGE III               0                2
  STAGE IIIA              0               40
  STAGE IIIB              0                7
  STAGE IIIC              0                6
  STAGE IV                0                2
  STAGE IVA               0                1
  STAGE IVB               0                2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               T1 T2 T3 T4
  EEF1A1 MUTATED    4  1  0  0
  EEF1A1 WILD-TYPE 73 47 50 11
D12V4, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  T1              4               73
  T2              1               47
  T3              0               50
  T4              0               11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V5, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     4   0
  EEF1A1 WILD-TYPE 115   3
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      4    0
  EEF1A1 WILD-TYPE  115    3
   clus
vv  EEF1A1 MUTATED EEF1A1 WILD-TYPE
  0              4              115
  1              0                3
[1] 2 2
[1] FALSE
                  vv
clus                M0  M1  MX
  EEF1A1 MUTATED     4   0   1
  EEF1A1 WILD-TYPE 134   4  45
D12V6, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  M0              4              134
  M1              0                4
  MX              1               45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     0   5
  EEF1A1 WILD-TYPE  68 115
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      0    5
  EEF1A1 WILD-TYPE   68  115
        clus
vv       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FEMALE              0               68
  MALE                5              115
[1] 2 2
[1] FALSE
                  vv
clus               FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  EEF1A1 MUTATED                         0                        5
  EEF1A1 WILD-TYPE                       1                      179
                  vv
clus               HEPATOCHOLANGIOCARCINOMA (MIXED)
  EEF1A1 MUTATED                                  0
  EEF1A1 WILD-TYPE                                3
D12V8, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                       0                1
  HEPATOCELLULAR CARCINOMA                      5              179
  HEPATOCHOLANGIOCARCINOMA (MIXED)              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                R0  R1  R2  RX
  EEF1A1 MUTATED     4   0   0   1
  EEF1A1 WILD-TYPE 151  10   1  15
D12V9, multiclass
    clus
vv   EEF1A1 MUTATED EEF1A1 WILD-TYPE
  R0              4              151
  R1              0               10
  R2              0                1
  RX              1               15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  EEF1A1 MUTATED                                  0     0
  EEF1A1 WILD-TYPE                                1    52
                  vv
clus               BLACK OR AFRICAN AMERICAN WHITE
  EEF1A1 MUTATED                           1     4
  EEF1A1 WILD-TYPE                        13   109
D12V10, multiclass
                                  clus
vv                                 EEF1A1 MUTATED EEF1A1 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE              0                1
  ASIAN                                         0               52
  BLACK OR AFRICAN AMERICAN                     1               13
  WHITE                                         4              109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                  cls
clus                 0   1
  EEF1A1 MUTATED     0   4
  EEF1A1 WILD-TYPE   5 165
[1] "tbl2"
                  cls
clus               [,1] [,2]
  EEF1A1 MUTATED      0    4
  EEF1A1 WILD-TYPE    5  165
                        clus
vv                       EEF1A1 MUTATED EEF1A1 WILD-TYPE
  HISPANIC OR LATINO                  0                5
  NOT HISPANIC OR LATINO              4              165
[1] 2 2
[1] FALSE

Clustering(13) Variable = KIF19 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  KIF19 MUTATED    4  5
  KIF19 WILD-TYPE 95 69
  KIF19 MUTATED KIF19 WILD-TYPE 
              9             164 
  KIF19 MUTATED KIF19 WILD-TYPE 
              5              69 
$`KIF19 MUTATED`
TCGA-BC-A10W TCGA-BC-A10Z TCGA-CC-5263 TCGA-DD-A3A0 TCGA-DD-A4NI TCGA-ED-A459 
        2.99         1.12         4.24        25.81        26.83        13.41 
TCGA-EP-A12J TCGA-EP-A2KA TCGA-UB-A7MB 
       18.74        11.74        17.29 

$`KIF19 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       27.91        37.32        10.13        27.52        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34        69.57         5.03        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5258 
       22.36         9.50        14.60        13.45         0.66         0.07 
TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 
        0.16         2.86         0.39         3.39         3.32         0.10 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        79.73        37.78        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.33       113.00         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.29        90.71        79.40        66.31        19.79        75.65 
TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK 
       12.95        45.11        49.15         6.02        29.16        18.35 
TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A1 
       13.64        21.14        55.69         5.62        19.76         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 
       70.06        17.59        20.12       102.74       107.11        13.78 
TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
        0.36        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL 
       30.97        14.63        30.15        30.51        39.78        56.25 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS 
       29.56        73.81       108.76        12.26         0.30        80.75 
TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E 
       78.84        10.98         9.30         7.56        10.98         1.45 
TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X 
       27.72       100.96        12.69        15.85        13.91        13.35 
TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP 
        0.23         0.20         0.20         0.20         0.20        13.15 
TCGA-ED-A82E TCGA-EP-A26S TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       13.41        19.99        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 
       22.85        14.40        32.45        23.97        19.10        27.88 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
        8.12         6.38         0.13         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.39         1.22        51.06        53.79        28.27        30.74 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86        21.53        25.64         5.92        19.53        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97        24.46        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.03         5.98         1.84         1.02         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
       24.36        12.72         9.57        16.67        18.38        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 
       20.71        58.88         4.44        21.01         2.04        21.04 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD 
       19.04        15.52        24.13        14.96        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  KIF19 MUTATED KIF19 WILD-TYPE 
           1.12            0.03 
  KIF19 MUTATED KIF19 WILD-TYPE 
          26.83          113.00 
  KIF19 MUTATED KIF19 WILD-TYPE 
         13.410          15.685 
[1] "1.1 - 26.8 (13.4)"  "0.0 - 113.0 (15.7)"
[1] "hr=" "2.2"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  KIF19 MUTATED         3        3         0          2          0          0
  KIF19 WILD-TYPE      71       40         2         38          7          6
                 vv
clus              STAGE IV STAGE IVA STAGE IVB
  KIF19 MUTATED          0         0         0
  KIF19 WILD-TYPE        2         1         2
D13V3, multiclass
            clus
vv           KIF19 MUTATED KIF19 WILD-TYPE
  STAGE I                3              71
  STAGE II               3              40
  STAGE III              0               2
  STAGE IIIA             2              38
  STAGE IIIB             0               7
  STAGE IIIC             0               6
  STAGE IV               0               2
  STAGE IVA              0               1
  STAGE IVB              0               2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              T1 T2 T3 T4
  KIF19 MUTATED    3  3  2  1
  KIF19 WILD-TYPE 74 45 48 10
D13V4, multiclass
    clus
vv   KIF19 MUTATED KIF19 WILD-TYPE
  T1             3              74
  T2             3              45
  T3             2              48
  T4             1              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V5, binary
                 cls
clus                0   1
  KIF19 MUTATED     3   0
  KIF19 WILD-TYPE 116   3
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      3    0
  KIF19 WILD-TYPE  116    3
   clus
vv  KIF19 MUTATED KIF19 WILD-TYPE
  0             3             116
  1             0               3
[1] 2 2
[1] FALSE
                 vv
clus               M0  M1  MX
  KIF19 MUTATED     4   0   5
  KIF19 WILD-TYPE 134   4  41
D13V6, multiclass
    clus
vv   KIF19 MUTATED KIF19 WILD-TYPE
  M0             4             134
  M1             0               4
  MX             5              41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                 cls
clus                0   1
  KIF19 MUTATED     2   7
  KIF19 WILD-TYPE  66 113
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      2    7
  KIF19 WILD-TYPE   66  113
        clus
vv       KIF19 MUTATED KIF19 WILD-TYPE
  FEMALE             2              66
  MALE               7             113
[1] 2 2
[1] FALSE
                 vv
clus              FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  KIF19 MUTATED                         0                        9
  KIF19 WILD-TYPE                       1                      175
                 vv
clus              HEPATOCHOLANGIOCARCINOMA (MIXED)
  KIF19 MUTATED                                  0
  KIF19 WILD-TYPE                                3
D13V8, multiclass
                                  clus
vv                                 KIF19 MUTATED KIF19 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                      0               1
  HEPATOCELLULAR CARCINOMA                     9             175
  HEPATOCHOLANGIOCARCINOMA (MIXED)             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               R0  R1  R2  RX
  KIF19 MUTATED     7   1   0   1
  KIF19 WILD-TYPE 148   9   1  15
D13V9, multiclass
    clus
vv   KIF19 MUTATED KIF19 WILD-TYPE
  R0             7             148
  R1             1               9
  R2             0               1
  RX             1              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  KIF19 MUTATED                                  0     3
  KIF19 WILD-TYPE                                1    49
                 vv
clus              BLACK OR AFRICAN AMERICAN WHITE
  KIF19 MUTATED                           1     5
  KIF19 WILD-TYPE                        13   108
D13V10, multiclass
                                  clus
vv                                 KIF19 MUTATED KIF19 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE             0               1
  ASIAN                                        3              49
  BLACK OR AFRICAN AMERICAN                    1              13
  WHITE                                        5             108
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, binary
                 cls
clus                0   1
  KIF19 MUTATED     0   9
  KIF19 WILD-TYPE   5 160
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KIF19 MUTATED      0    9
  KIF19 WILD-TYPE    5  160
                        clus
vv                       KIF19 MUTATED KIF19 WILD-TYPE
  HISPANIC OR LATINO                 0               5
  NOT HISPANIC OR LATINO             9             160
[1] 2 2
[1] FALSE

Clustering(14) Variable = GNAS MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  GNAS MUTATED    5  1
  GNAS WILD-TYPE 94 73
  GNAS MUTATED GNAS WILD-TYPE 
             6            167 
  GNAS MUTATED GNAS WILD-TYPE 
             1             73 
$`GNAS MUTATED`
TCGA-DD-A118 TCGA-FV-A3R3 TCGA-G3-A25V TCGA-G3-A7M7 TCGA-K7-A5RF TCGA-MI-A75G 
      113.00         0.13        28.27         5.98        20.75        18.38 

$`GNAS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       79.73        37.78        83.57        53.33         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.76        51.29        90.71        79.40        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
       19.79        75.65        12.95        45.11        49.15         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
       29.16        18.35        13.64        21.14        55.69         5.62 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
       19.76        25.81         7.66        70.06        17.59        20.12 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
      102.74       107.11        13.78         0.36        30.61        33.14 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
       32.52        73.38        21.70        30.97        14.63        30.15 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
       26.83        30.51        39.78        56.25        29.56        73.81 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
      108.76        12.26         0.30        80.75        78.84        10.98 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
        9.30         7.56        10.98         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP 
       27.88         8.12         6.38         0.03         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Y 
        0.39         1.22        51.06        53.79        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       11.97        24.46        20.42        17.10         7.76        12.03 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RG TCGA-K7-A6G5 
        1.84         1.02         2.66        37.71        17.06         4.01 
TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C 
        2.14        11.84        13.38        24.36        12.72         9.57 
TCGA-MI-A75E TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       16.67        12.85        20.71        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA 
        2.04        21.04        19.04        15.52        24.13        14.96 
TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       17.29        14.40         1.71        15.98         7.04 

  GNAS MUTATED GNAS WILD-TYPE 
          0.13           0.03 
  GNAS MUTATED GNAS WILD-TYPE 
        113.00         108.76 
  GNAS MUTATED GNAS WILD-TYPE 
        19.565         14.960 
[1] "0.1 - 113.0 (19.6)" "0.0 - 108.8 (15.0)"
[1] "hr=" "3.9"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  GNAS MUTATED         4        3         0          0          0          0
  GNAS WILD-TYPE      70       40         2         40          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  GNAS MUTATED          0         0         0
  GNAS WILD-TYPE        2         1         2
D14V3, multiclass
            clus
vv           GNAS MUTATED GNAS WILD-TYPE
  STAGE I               4             70
  STAGE II              3             40
  STAGE III             0              2
  STAGE IIIA            0             40
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  GNAS MUTATED    4  3  0  0
  GNAS WILD-TYPE 73 45 50 11
D14V4, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  T1            4             73
  T2            3             45
  T3            0             50
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V5, binary
                cls
clus               0   1
  GNAS MUTATED     4   0
  GNAS WILD-TYPE 115   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      4    0
  GNAS WILD-TYPE  115    3
   clus
vv  GNAS MUTATED GNAS WILD-TYPE
  0            4            115
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  GNAS MUTATED     4   0   3
  GNAS WILD-TYPE 134   4  43
D14V6, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  M0            4            134
  M1            0              4
  MX            3             43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                cls
clus               0   1
  GNAS MUTATED     2   5
  GNAS WILD-TYPE  66 115
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      2    5
  GNAS WILD-TYPE   66  115
        clus
vv       GNAS MUTATED GNAS WILD-TYPE
  FEMALE            2             66
  MALE              5            115
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  GNAS MUTATED                         0                        7
  GNAS WILD-TYPE                       1                      177
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  GNAS MUTATED                                  0
  GNAS WILD-TYPE                                3
D14V8, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    7            177
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  GNAS MUTATED     7   0   0   0
  GNAS WILD-TYPE 148  10   1  16
D14V9, multiclass
    clus
vv   GNAS MUTATED GNAS WILD-TYPE
  R0            7            148
  R1            0             10
  R2            0              1
  RX            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  GNAS MUTATED                                  0     1
  GNAS WILD-TYPE                                1    51
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  GNAS MUTATED                           0     6
  GNAS WILD-TYPE                        14   107
D14V10, multiclass
                                  clus
vv                                 GNAS MUTATED GNAS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             51
  BLACK OR AFRICAN AMERICAN                   0             14
  WHITE                                       6            107
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, binary
                cls
clus               0   1
  GNAS MUTATED     0   7
  GNAS WILD-TYPE   5 162
[1] "tbl2"
                cls
clus             [,1] [,2]
  GNAS MUTATED      0    7
  GNAS WILD-TYPE    5  162
                        clus
vv                       GNAS MUTATED GNAS WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            7            162
[1] 2 2
[1] FALSE

Clustering(15) Variable = F5 MUTATION ANALYSIS
D15V1, survival
              sevent
clus2           0  1
  F5 MUTATED    2  2
  F5 WILD-TYPE 97 72
  F5 MUTATED F5 WILD-TYPE 
           4          169 
  F5 MUTATED F5 WILD-TYPE 
           2           72 
$`F5 MUTATED`
TCGA-ED-A459 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-UB-A7MB 
       13.41        10.98        22.85        17.29 

$`F5 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        30.97        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F 
       10.98         9.30         7.56        10.98         1.45        27.72 
TCGA-DD-A73G TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
      100.96        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       18.74        19.99        11.74         0.62         9.96        11.93 
TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       14.40        32.45        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       11.97        24.46        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        5.98         1.84         1.02         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.72         9.57        16.67        18.38        12.85        20.71 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME 
       15.52        24.13        14.96        14.40         1.71        15.98 
TCGA-UB-A7MF 
        7.04 

  F5 MUTATED F5 WILD-TYPE 
       10.98         0.03 
  F5 MUTATED F5 WILD-TYPE 
       22.85       113.00 
  F5 MUTATED F5 WILD-TYPE 
       15.35        15.52 
[1] "11.0 - 22.9 (15.3)" "0.0 - 113.0 (15.5)"
[1] "hr=" "1.7"
D15V2, continuous
              vv
clus           STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  F5 MUTATED         2        2         0          0          0          0
  F5 WILD-TYPE      72       41         2         40          7          6
              vv
clus           STAGE IV STAGE IVA STAGE IVB
  F5 MUTATED          0         0         0
  F5 WILD-TYPE        2         1         2
D15V3, multiclass
            clus
vv           F5 MUTATED F5 WILD-TYPE
  STAGE I             2           72
  STAGE II            2           41
  STAGE III           0            2
  STAGE IIIA          0           40
  STAGE IIIB          0            7
  STAGE IIIC          0            6
  STAGE IV            0            2
  STAGE IVA           0            1
  STAGE IVB           0            2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           T1 T2 T3 T4
  F5 MUTATED    2  2  0  0
  F5 WILD-TYPE 75 46 50 11
D15V4, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  T1          2           75
  T2          2           46
  T3          0           50
  T4          0           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V5, binary
              cls
clus             0   1
  F5 MUTATED     1   0
  F5 WILD-TYPE 118   3
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      1    0
  F5 WILD-TYPE  118    3
   clus
vv  F5 MUTATED F5 WILD-TYPE
  0          1          118
  1          0            3
[1] 2 2
[1] FALSE
              vv
clus            M0  M1  MX
  F5 MUTATED     1   0   3
  F5 WILD-TYPE 137   4  43
D15V6, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  M0          1          137
  M1          0            4
  MX          3           43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
              cls
clus             0   1
  F5 MUTATED     1   3
  F5 WILD-TYPE  67 117
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      1    3
  F5 WILD-TYPE   67  117
        clus
vv       F5 MUTATED F5 WILD-TYPE
  FEMALE          1           67
  MALE            3          117
[1] 2 2
[1] FALSE
              vv
clus           FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  F5 MUTATED                         0                        4
  F5 WILD-TYPE                       1                      180
              vv
clus           HEPATOCHOLANGIOCARCINOMA (MIXED)
  F5 MUTATED                                  0
  F5 WILD-TYPE                                3
D15V8, multiclass
                                  clus
vv                                 F5 MUTATED F5 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                   0            1
  HEPATOCELLULAR CARCINOMA                  4          180
  HEPATOCHOLANGIOCARCINOMA (MIXED)          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            R0  R1  R2  RX
  F5 MUTATED     4   0   0   0
  F5 WILD-TYPE 151  10   1  16
D15V9, multiclass
    clus
vv   F5 MUTATED F5 WILD-TYPE
  R0          4          151
  R1          0           10
  R2          0            1
  RX          0           16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
              vv
clus           AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  F5 MUTATED                                  0     1                         0
  F5 WILD-TYPE                                1    51                        14
              vv
clus           WHITE
  F5 MUTATED       3
  F5 WILD-TYPE   110
D15V10, multiclass
                                  clus
vv                                 F5 MUTATED F5 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE          0            1
  ASIAN                                     1           51
  BLACK OR AFRICAN AMERICAN                 0           14
  WHITE                                     3          110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, binary
              cls
clus             0   1
  F5 MUTATED     0   4
  F5 WILD-TYPE   5 165
[1] "tbl2"
              cls
clus           [,1] [,2]
  F5 MUTATED      0    4
  F5 WILD-TYPE    5  165
                        clus
vv                       F5 MUTATED F5 WILD-TYPE
  HISPANIC OR LATINO              0            5
  NOT HISPANIC OR LATINO          4          165
[1] 2 2
[1] FALSE

Clustering(16) Variable = PTEN MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  PTEN MUTATED    2  3
  PTEN WILD-TYPE 97 71
  PTEN MUTATED PTEN WILD-TYPE 
             5            168 
  PTEN MUTATED PTEN WILD-TYPE 
             3             71 
$`PTEN MUTATED`
TCGA-BC-A112 TCGA-DD-A11C TCGA-DD-A3A0 TCGA-DD-A4NE TCGA-QA-A7B7 
        5.03        21.76        25.81        21.70         2.04 

$`PTEN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.78        83.57        53.33       113.00         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 
        7.66        70.06        17.59        20.12       102.74       107.11 
TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND 
       13.78         0.36        30.61        33.14        32.52        73.38 
TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       30.97        14.63        30.15        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       56.25        29.56        73.81       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       80.75        78.84        10.98         9.30         7.56        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG 
        1.45        27.72       100.96        13.41        12.69        15.85 
TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ 
       13.91        13.35         0.23         0.20         0.20         0.20 
TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.20        13.15        13.41        18.74        19.99        11.74 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       10.98         0.62         9.96        11.93        22.85        14.40 
TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 
       32.45        23.97        19.10        27.88         8.12         6.38 
TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S 
        0.13         0.03         0.33        60.36         0.39         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       51.06        53.79        28.27        30.74        14.86        21.53 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ 
       25.64         5.92        19.53        19.23        14.70        11.97 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-A7M7 
       24.46        20.42        17.10         7.76        12.03         5.98 
TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        1.84         1.02         2.66        37.71        20.75        17.06 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
        4.01         2.14        11.84        13.38        24.36        12.72 
TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
        9.57        16.67        18.38        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 
        4.44        21.01        21.04        19.04        15.52        24.13 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       14.96        17.29        14.40         1.71        15.98         7.04 

  PTEN MUTATED PTEN WILD-TYPE 
          2.04           0.03 
  PTEN MUTATED PTEN WILD-TYPE 
         25.81         113.00 
  PTEN MUTATED PTEN WILD-TYPE 
         21.70          15.24 
[1] "2.0 - 25.8 (21.7)"  "0.0 - 113.0 (15.2)"
[1] "hr=" "2"  
D16V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  PTEN MUTATED         2        1         0          1          0          0
  PTEN WILD-TYPE      72       42         2         39          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  PTEN MUTATED          0         0         0
  PTEN WILD-TYPE        2         1         2
D16V3, multiclass
            clus
vv           PTEN MUTATED PTEN WILD-TYPE
  STAGE I               2             72
  STAGE II              1             42
  STAGE III             0              2
  STAGE IIIA            1             39
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  PTEN MUTATED    2  1  2  0
  PTEN WILD-TYPE 75 47 48 11
D16V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            2             75
  T2            1             47
  T3            2             48
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V5, binary
                cls
clus               0   1
  PTEN MUTATED     2   0
  PTEN WILD-TYPE 117   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      2    0
  PTEN WILD-TYPE  117    3
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            2            117
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  PTEN MUTATED     3   0   2
  PTEN WILD-TYPE 135   4  44
D16V6, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  M0            3            135
  M1            0              4
  MX            2             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                cls
clus               0   1
  PTEN MUTATED     1   4
  PTEN WILD-TYPE  67 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    4
  PTEN WILD-TYPE   67  116
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            1             67
  MALE              4            116
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  PTEN MUTATED                         0                        5
  PTEN WILD-TYPE                       1                      179
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  PTEN MUTATED                                  0
  PTEN WILD-TYPE                                3
D16V8, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    5            179
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  PTEN MUTATED     3   0   0   2
  PTEN WILD-TYPE 152  10   1  14
D16V9, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  R0            3            152
  R1            0             10
  R2            0              1
  RX            2             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  PTEN MUTATED                                  0     0
  PTEN WILD-TYPE                                1    52
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED                           1     4
  PTEN WILD-TYPE                        13   109
D16V10, multiclass
                                  clus
vv                                 PTEN MUTATED PTEN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       0             52
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                       4            109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, binary
                cls
clus               0   1
  PTEN MUTATED     1   4
  PTEN WILD-TYPE   4 165
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      1    4
  PTEN WILD-TYPE    4  165
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                1              4
  NOT HISPANIC OR LATINO            4            165
[1] 2 2
[1] FALSE

Clustering(17) Variable = HIST1H1C MUTATION ANALYSIS
D17V1, survival
                    sevent
clus2                 0  1
  HIST1H1C MUTATED    5  0
  HIST1H1C WILD-TYPE 94 74
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 5                168 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
                 0                 74 
$`HIST1H1C MUTATED`
TCGA-DD-A73D TCGA-G3-A3CJ TCGA-MI-A75E TCGA-MI-A75G TCGA-UB-A7MA 
       10.98        19.53        16.67        18.38        14.96 

$`HIST1H1C WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        44.42 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP 
       13.84         0.26        22.36         9.50        14.60        13.45 
TCGA-BW-A5NO TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        0.66         0.07         0.16         2.86         0.39         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        4.24         3.32         0.10         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       79.73        37.78        83.57        53.33       113.00         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.76        51.29        90.71        79.40 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH 
       66.31        19.79        75.65        12.95        45.11        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X 
        6.02        29.16        18.35        13.64        21.14        55.69 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 
        5.62        19.76        25.81         7.66        70.06        17.59 
TCGA-DD-A3A4 TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 
       20.12       102.74       107.11        13.78         0.36        30.61 
TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG 
       33.14        32.52        73.38        21.70        30.97        14.63 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN 
       30.15        26.83        30.51        39.78        56.25        29.56 
TCGA-DD-A4NO TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV 
       73.81       108.76        12.26         0.30        80.75        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
       10.98         9.30         7.56         1.45        27.72       100.96 
TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y 
       13.41        12.69        15.85        13.91        13.35         0.23 
TCGA-ED-A7PX TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E 
        0.20         0.20         0.20         0.20        13.15        13.41 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       18.74        19.99        11.74        10.98         0.62         9.96 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.93        22.85        14.40        32.45        23.97        19.10 
TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 
       27.88         8.12         6.38         0.13         0.03         0.33 
TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       60.36         0.39         1.22        51.06        53.79        28.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       30.74        14.86        21.53        25.64         5.92        19.23 
TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC 
       14.70        11.97        24.46        20.42        17.10         7.76 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 
       12.03         5.98         1.84         1.02         2.66        37.71 
TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 
       20.75        17.06         4.01         2.14        11.84        13.38 
TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
       24.36        12.72         9.57        12.85        20.71        58.88 
TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SK 
        4.44        21.01         2.04        21.04        19.04        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
       24.13        17.29        14.40         1.71        15.98         7.04 

  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             10.98               0.03 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             19.53             113.00 
  HIST1H1C MUTATED HIST1H1C WILD-TYPE 
             16.67              15.19 
[1] "11.0 - 19.5 (16.7)" "0.0 - 113.0 (15.2)"
[1] "hr="     "9400000"
D17V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB
  HIST1H1C MUTATED         0        4         0          0          0
  HIST1H1C WILD-TYPE      74       39         2         40          7
                    vv
clus                 STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  HIST1H1C MUTATED            1        0         0         0
  HIST1H1C WILD-TYPE          5        2         1         2
D17V3, multiclass
            clus
vv           HIST1H1C MUTATED HIST1H1C WILD-TYPE
  STAGE I                   0                 74
  STAGE II                  4                 39
  STAGE III                 0                  2
  STAGE IIIA                0                 40
  STAGE IIIB                0                  7
  STAGE IIIC                1                  5
  STAGE IV                  0                  2
  STAGE IVA                 0                  1
  STAGE IVB                 0                  2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  HIST1H1C MUTATED    0  4  0  1
  HIST1H1C WILD-TYPE 77 44 50 10
D17V4, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  T1                0                 77
  T2                4                 44
  T3                0                 50
  T4                1                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     4   0
  HIST1H1C WILD-TYPE 115   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      4    0
  HIST1H1C WILD-TYPE  115    3
   clus
vv  HIST1H1C MUTATED HIST1H1C WILD-TYPE
  0                4                115
  1                0                  3
[1] 2 2
[1] FALSE
                    vv
clus                  M0  M1  MX
  HIST1H1C MUTATED     4   0   1
  HIST1H1C WILD-TYPE 134   4  45
D17V6, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  M0                4                134
  M1                0                  4
  MX                1                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     2   3
  HIST1H1C WILD-TYPE  66 117
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      2    3
  HIST1H1C WILD-TYPE   66  117
        clus
vv       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FEMALE                2                 66
  MALE                  3                117
[1] 2 2
[1] FALSE
                    vv
clus                 FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  HIST1H1C MUTATED                         0                        4
  HIST1H1C WILD-TYPE                       1                      180
                    vv
clus                 HEPATOCHOLANGIOCARCINOMA (MIXED)
  HIST1H1C MUTATED                                  1
  HIST1H1C WILD-TYPE                                2
D17V8, multiclass
                                  clus
vv                                 HIST1H1C MUTATED HIST1H1C WILD-TYPE
  FIBROLAMELLAR CARCINOMA                         0                  1
  HEPATOCELLULAR CARCINOMA                        4                180
  HEPATOCHOLANGIOCARCINOMA (MIXED)                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                  R0  R1  R2  RX
  HIST1H1C MUTATED     4   1   0   0
  HIST1H1C WILD-TYPE 151   9   1  16
D17V9, multiclass
    clus
vv   HIST1H1C MUTATED HIST1H1C WILD-TYPE
  R0                4                151
  R1                1                  9
  R2                0                  1
  RX                0                 16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  HIST1H1C MUTATED                                  1     0
  HIST1H1C WILD-TYPE                                0    52
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  HIST1H1C MUTATED                           0     4
  HIST1H1C WILD-TYPE                        14   109
D17V10, multiclass
                                  clus
vv                                 HIST1H1C MUTATED HIST1H1C WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  0
  ASIAN                                           0                 52
  BLACK OR AFRICAN AMERICAN                       0                 14
  WHITE                                           4                109
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                    cls
clus                   0   1
  HIST1H1C MUTATED     0   5
  HIST1H1C WILD-TYPE   5 164
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  HIST1H1C MUTATED      0    5
  HIST1H1C WILD-TYPE    5  164
                        clus
vv                       HIST1H1C MUTATED HIST1H1C WILD-TYPE
  HISPANIC OR LATINO                    0                  5
  NOT HISPANIC OR LATINO                5                164
[1] 2 2
[1] FALSE

Clustering(18) Variable = DLK2 MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  DLK2 MUTATED    0  3
  DLK2 WILD-TYPE 99 71
  DLK2 MUTATED DLK2 WILD-TYPE 
             3            170 
  DLK2 MUTATED DLK2 WILD-TYPE 
             3             71 
$`DLK2 MUTATED`
TCGA-BC-A112 TCGA-DD-A115 TCGA-ES-A2HT 
        5.03        83.57        14.40 

$`DLK2 WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       27.91        37.32        10.13        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        44.42        13.84 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BD-A3EP TCGA-BW-A5NO 
        0.26        22.36         9.50        14.60        13.45         0.66 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
        0.07         0.16         2.86         0.39         3.39         4.24 
TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 
        3.32         0.10         0.07         0.10         0.13        79.73 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.78        53.33       113.00         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.76        51.29        90.71        79.40        66.31        19.79 
TCGA-DD-A1ED TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       75.65        12.95        45.11        49.15         6.02        29.16 
TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y TCGA-DD-A39Z 
       18.35        13.64        21.14        55.69         5.62        19.76 
TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       25.81         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB 
      107.11        13.78         0.36        30.61        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH TCGA-DD-A4NI 
       73.38        21.70        30.97        14.63        30.15        26.83 
TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NP 
       30.51        39.78        56.25        29.56        73.81       108.76 
TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       12.26         0.30        80.75        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G TCGA-ED-A459 
        7.56        10.98         1.45        27.72       100.96        13.41 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
       12.69        15.85        13.91        13.35         0.23         0.20 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-EP-A12J 
        0.20         0.20         0.20        13.15        13.41        18.74 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
       19.99        11.74        10.98         0.62         9.96        11.93 
TCGA-ES-A2HS TCGA-FV-A23B TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 
       22.85        32.45        23.97        19.10        27.88         8.12 
TCGA-FV-A3R2 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ 
        6.38         0.13         0.03         0.33        60.36         0.39 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y 
        1.22        51.06        53.79        28.27        30.74        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
       21.53        25.64         5.92        19.53        19.23        14.70 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 
       11.97        24.46        20.42        17.10         7.76        12.03 
TCGA-G3-A7M7 TCGA-G3-A7M9 TCGA-GJ-A6C0 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
        5.98         1.84         1.02         2.66        37.71        20.75 
TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 
       17.06         4.01         2.14        11.84        13.38        24.36 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I 
       12.72         9.57        16.67        18.38        12.85        20.71 
TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF 
       58.88         4.44        21.01         2.04        21.04        19.04 
TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD 
       15.52        24.13        14.96        17.29        14.40         1.71 
TCGA-UB-A7ME TCGA-UB-A7MF 
       15.98         7.04 

  DLK2 MUTATED DLK2 WILD-TYPE 
          5.03           0.03 
  DLK2 MUTATED DLK2 WILD-TYPE 
         83.57         113.00 
  DLK2 MUTATED DLK2 WILD-TYPE 
        14.400         15.685 
[1] "5.0 - 83.6 (14.4)"  "0.0 - 113.0 (15.7)"
[1] "hr=" "1.7"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DLK2 MUTATED         1        0         0          2          0          0
  DLK2 WILD-TYPE      73       43         2         38          7          6
                vv
clus             STAGE IV STAGE IVA STAGE IVB
  DLK2 MUTATED          0         0         0
  DLK2 WILD-TYPE        2         1         2
D18V3, multiclass
            clus
vv           DLK2 MUTATED DLK2 WILD-TYPE
  STAGE I               1             73
  STAGE II              0             43
  STAGE III             0              2
  STAGE IIIA            2             38
  STAGE IIIB            0              7
  STAGE IIIC            0              6
  STAGE IV              0              2
  STAGE IVA             0              1
  STAGE IVB             0              2
[1] 9 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             T1 T2 T3 T4
  DLK2 MUTATED    1  0  3  0
  DLK2 WILD-TYPE 76 48 47 11
D18V4, multiclass
    clus
vv   DLK2 MUTATED DLK2 WILD-TYPE
  T1            1             76
  T2            0             48
  T3            3             47
  T4            0             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V5, binary
                cls
clus               0   1
  DLK2 MUTATED     2   0
  DLK2 WILD-TYPE 117   3
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      2    0
  DLK2 WILD-TYPE  117    3
   clus
vv  DLK2 MUTATED DLK2 WILD-TYPE
  0            2            117
  1            0              3
[1] 2 2
[1] FALSE
                vv
clus              M0  M1  MX
  DLK2 MUTATED     2   0   2
  DLK2 WILD-TYPE 136   4  44
D18V6, multiclass
    clus
vv   DLK2 MUTATED DLK2 WILD-TYPE
  M0            2            136
  M1            0              4
  MX            2             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                cls
clus               0   1
  DLK2 MUTATED     0   4
  DLK2 WILD-TYPE  68 116
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      0    4
  DLK2 WILD-TYPE   68  116
        clus
vv       DLK2 MUTATED DLK2 WILD-TYPE
  FEMALE            0             68
  MALE              4            116
[1] 2 2
[1] FALSE
                vv
clus             FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  DLK2 MUTATED                         0                        4
  DLK2 WILD-TYPE                       1                      180
                vv
clus             HEPATOCHOLANGIOCARCINOMA (MIXED)
  DLK2 MUTATED                                  0
  DLK2 WILD-TYPE                                3
D18V8, multiclass
                                  clus
vv                                 DLK2 MUTATED DLK2 WILD-TYPE
  FIBROLAMELLAR CARCINOMA                     0              1
  HEPATOCELLULAR CARCINOMA                    4            180
  HEPATOCHOLANGIOCARCINOMA (MIXED)            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              R0  R1  R2  RX
  DLK2 MUTATED     4   0   0   0
  DLK2 WILD-TYPE 151  10   1  16
D18V9, multiclass
    clus
vv   DLK2 MUTATED DLK2 WILD-TYPE
  R0            4            151
  R1            0             10
  R2            0              1
  RX            0             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DLK2 MUTATED                                  0     1
  DLK2 WILD-TYPE                                1    51
                vv
clus             BLACK OR AFRICAN AMERICAN WHITE
  DLK2 MUTATED                           1     2
  DLK2 WILD-TYPE                        13   111
D18V10, multiclass
                                  clus
vv                                 DLK2 MUTATED DLK2 WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE            0              1
  ASIAN                                       1             51
  BLACK OR AFRICAN AMERICAN                   1             13
  WHITE                                       2            111
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, binary
                cls
clus               0   1
  DLK2 MUTATED     0   3
  DLK2 WILD-TYPE   5 166
[1] "tbl2"
                cls
clus             [,1] [,2]
  DLK2 MUTATED      0    3
  DLK2 WILD-TYPE    5  166
                        clus
vv                       DLK2 MUTATED DLK2 WILD-TYPE
  HISPANIC OR LATINO                0              5
  NOT HISPANIC OR LATINO            3            166
[1] 2 2
[1] FALSE
