[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"        "-oTBLCA-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/BLCA-TP/11541262/BLCA-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/10686699/transformed.cor.cli.txt"

nPatients in clinical file=281, in cluster file=130, common to both=130
[1]  35 130
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            64             66 
  TP53 MUTATED TP53 WILD-TYPE 
            64             66 
[1] "KDM6A MUTATION ANALYSIS"
[1] 3
  KDM6A MUTATED KDM6A WILD-TYPE 
             31              99 
  KDM6A MUTATED KDM6A WILD-TYPE 
             31              99 
[1] "RB1 MUTATION ANALYSIS"
[1] 3
  RB1 MUTATED RB1 WILD-TYPE 
           17           113 
  RB1 MUTATED RB1 WILD-TYPE 
           17           113 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              32               98 
  ARID1A MUTATED ARID1A WILD-TYPE 
              32               98 
[1] "CDKN1A MUTATION ANALYSIS"
[1] 3
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              18              112 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              18              112 
[1] "MLL2 MUTATION ANALYSIS"
[1] 3
  MLL2 MUTATED MLL2 WILD-TYPE 
            36             94 
  MLL2 MUTATED MLL2 WILD-TYPE 
            36             94 
[1] "ELF3 MUTATION ANALYSIS"
[1] 3
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            119 
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            119 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             114 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             114 
[1] "CDKN2A MUTATION ANALYSIS"
[1] 3
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              123 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              123 
[1] "STAG2 MUTATION ANALYSIS"
[1] 3
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             116 
  STAG2 MUTATED STAG2 WILD-TYPE 
             14             116 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              119 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              119 
[1] "ERCC2 MUTATION ANALYSIS"
[1] 3
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             16             114 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             16             114 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             117 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             117 
[1] "RHOB MUTATION ANALYSIS"
[1] 3
  RHOB MUTATED RHOB WILD-TYPE 
             7            123 
  RHOB MUTATED RHOB WILD-TYPE 
             7            123 
[1] "TSC1 MUTATION ANALYSIS"
[1] 3
  TSC1 MUTATED TSC1 WILD-TYPE 
            11            119 
  TSC1 MUTATED TSC1 WILD-TYPE 
            11            119 
[1] "FOXQ1 MUTATION ANALYSIS"
[1] 3
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              7             123 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              7             123 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              104 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              104 
[1] "RXRA MUTATION ANALYSIS"
[1] 3
  RXRA MUTATED RXRA WILD-TYPE 
            12            118 
  RXRA MUTATED RXRA WILD-TYPE 
            12            118 
[1] "CREBBP MUTATION ANALYSIS"
[1] 3
  CREBBP MUTATED CREBBP WILD-TYPE 
              17              113 
  CREBBP MUTATED CREBBP WILD-TYPE 
              17              113 
[1] "ERBB3 MUTATION ANALYSIS"
[1] 3
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             116 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             116 
[1] "FAT1 MUTATION ANALYSIS"
[1] 3
  FAT1 MUTATED FAT1 WILD-TYPE 
            15            115 
  FAT1 MUTATED FAT1 WILD-TYPE 
            15            115 
[1] "MLL MUTATION ANALYSIS"
[1] 3
  MLL MUTATED MLL WILD-TYPE 
           18           112 
  MLL MUTATED MLL WILD-TYPE 
           18           112 
[1] "HRAS MUTATION ANALYSIS"
[1] 3
  HRAS MUTATED HRAS WILD-TYPE 
             6            124 
  HRAS MUTATED HRAS WILD-TYPE 
             6            124 
[1] "ACRC MUTATION ANALYSIS"
[1] 3
  ACRC MUTATED ACRC WILD-TYPE 
             4            126 
  ACRC MUTATED ACRC WILD-TYPE 
             4            126 
[1] "TXNIP MUTATION ANALYSIS"
[1] 3
  TXNIP MUTATED TXNIP WILD-TYPE 
              9             121 
  TXNIP MUTATED TXNIP WILD-TYPE 
              9             121 
[1] "ECM1 MUTATION ANALYSIS"
[1] 3
  ECM1 MUTATED ECM1 WILD-TYPE 
             5            125 
  ECM1 MUTATED ECM1 WILD-TYPE 
             5            125 
[1] "KLF5 MUTATION ANALYSIS"
[1] 3
  KLF5 MUTATED KLF5 WILD-TYPE 
            10            120 
  KLF5 MUTATED KLF5 WILD-TYPE 
            10            120 
[1] "RBM26 MUTATION ANALYSIS"
[1] 3
  RBM26 MUTATED RBM26 WILD-TYPE 
              9             121 
  RBM26 MUTATED RBM26 WILD-TYPE 
              9             121 
[1] "RAD51C MUTATION ANALYSIS"
[1] 3
  RAD51C MUTATED RAD51C WILD-TYPE 
               4              126 
  RAD51C MUTATED RAD51C WILD-TYPE 
               4              126 
[1] "CEP192 MUTATION ANALYSIS"
[1] 3
  CEP192 MUTATED CEP192 WILD-TYPE 
               5              125 
  CEP192 MUTATED CEP192 WILD-TYPE 
               5              125 
[1] "ASXL2 MUTATION ANALYSIS"
[1] 3
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              9             121 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              9             121 
[1] "PSIP1 MUTATION ANALYSIS"
[1] 3
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              7             123 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              7             123 
[1] "ZNF513 MUTATION ANALYSIS"
[1] 3
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               7              123 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               7              123 
[1] "FOXA1 MUTATION ANALYSIS"
[1] 3
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              7             123 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              7             123 
[1] "TRIP11 MUTATION ANALYSIS"
[1] 3
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               5              125 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               5              125 
[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] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 130 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
        1219           NA           NA           NA           NA          363 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
          NA           NA           NA           NA           NA           NA 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
          NA           NA           NA          170          111           NA 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
         390           63          469          873           59           89 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CF-A3MF 
         700           NA           14           13           21           NA 
TCGA-CF-A3MG TCGA-CF-A3MH TCGA-CF-A3MI TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
          NA           NA           NA           NA           NA          219 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
         166          158          496           77           NA         2020 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
         560          578          271         3981         3420          491 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
         536          475           55          322           NA         3767 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
        2656           67          121          238           NA          319 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
        1529          648          609           NA          252           NA 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
        4283         1460         1326          750            3          392 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
          NA          209           NA          378          363         1397 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
          NA          683          186          390           NA          401 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
          NA           NA           60          462          106          124 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
          NA          679         1884          931          173         1072 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
         525          214           NA           26           88           68 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
         481          137          484          428          540           34 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV 
         235           64           95          638          344          134 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QG TCGA-GV-A3QH 
         195          187          173          232           NA          237 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
         126          203          195          580           46          205 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1174          266          105          142 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=92,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	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:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=32,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=14,	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] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "NUMBER.OF.LYMPH.NODES"       "RACE"                       
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 130 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 1 30 65 17 
[1] "table(vv)"
vv
T1+T2    T3    T4 
   31    65    17 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 1 30 65 17 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


T1+T2    T3    T4 
   31    65    17 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 N3 
74 13 24  6 
[1] "table(vv)"
vv
N0 N1 N2 N3 
74 13 24  6 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 N3 
74 13 24  6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


N0 N1 N2 N3 
74 13 24  6 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=32, binary=FALSE, numeric=TRUE
NUMBER.OF.LYMPH.NODES, nv=12, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = TP53 MUTATION ANALYSIS
D1V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   39 25
  TP53 WILD-TYPE 41 20
  TP53 MUTATED TP53 WILD-TYPE 
            64             61 
  TP53 MUTATED TP53 WILD-TYPE 
            25             20 
$`TP53 MUTATED`
TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20R 
        2.66         6.74        19.04        32.84        12.16         5.06 
TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-C4-A0F7 
       14.96         5.59         3.65         4.67        12.82         2.04 
TCGA-CF-A1HS TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB 
        0.43         5.46         2.53         2.14        66.41         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
      130.88       112.44         7.79        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3X1 
        7.82         8.22        50.27        20.02         9.67        48.00 
TCGA-E5-A2PC TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
       43.59         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
       24.30        22.45         5.52        13.18        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES 
       15.19         3.48         4.08        30.61        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         0.85        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OS TCGA-GV-A3JW TCGA-GV-A3JX 
       17.75         1.12         7.73        20.98         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QK TCGA-GV-A40G 
        5.69         7.79         6.67        19.07 

$`TP53 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20P TCGA-BT-A20Q 
       40.08         7.33         6.58        11.93        17.88        19.50 
TCGA-BT-A20T TCGA-BT-A20W TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 
       14.89         8.35         2.07        15.42        28.70         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.93        23.01         0.46         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AE 
        7.20         5.19        16.31        18.41        19.00        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IQ 
       17.62        15.62         1.81        10.59       123.85        10.49 
TCGA-DK-A3IT TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E7-A3X6 TCGA-E7-A3Y1 
       21.30         8.28        10.55       140.81        24.66         0.10 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SQ TCGA-FT-A3EE 
       12.89         8.94         6.12        12.82        46.78         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3RD 
       22.32        61.94         5.69         2.89         2.24        14.07 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QF TCGA-GV-A3QI 
        2.10         3.12        11.31         4.41         7.63         4.14 
TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  TP53 MUTATED TP53 WILD-TYPE 
          0.43           0.10 
  TP53 MUTATED TP53 WILD-TYPE 
        130.88         140.81 
  TP53 MUTATED TP53 WILD-TYPE 
         8.565          8.940 
[1] "0.4 - 130.9 (8.6)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.1"
D1V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         0       20        18       25
  TP53 WILD-TYPE       1       17        26       19
D1V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              0              1
  STAGE II            20             17
  STAGE III           18             26
  STAGE IV            25             19
[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             T1+T2 T3 T4
  TP53 MUTATED      16 29 10
  TP53 WILD-TYPE    15 36  7
D1V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1+T2           16             15
  T3              29             36
  T4              10              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TP53 MUTATED   31  7 13  5
  TP53 WILD-TYPE 43  6 11  1
D1V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           31             43
  N1            7              6
  N2           13             11
  N3            5              1
[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             M0 M1 MX
  TP53 MUTATED   34  2 27
  TP53 WILD-TYPE 42  2 22
D1V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           34             42
  M1            2              2
  MX           27             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                cls
clus              0  1
  TP53 MUTATED   15 49
  TP53 WILD-TYPE 17 49
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     15   49
  TP53 WILD-TYPE   17   49
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           15             17
  MALE             49             49
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
D1V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       2                         3    57
  TP53 WILD-TYPE     6                         3    50
D1V11, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                2              6
  BLACK OR AFRICAN AMERICAN            3              3
  WHITE                               57             50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = KDM6A MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  KDM6A MUTATED   19 12
  KDM6A WILD-TYPE 61 33
  KDM6A MUTATED KDM6A WILD-TYPE 
             31              94 
  KDM6A MUTATED KDM6A WILD-TYPE 
             12              33 
$`KDM6A MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-CF-A1HS 
        6.58        14.89         5.59         3.65         4.67         0.43 
TCGA-CU-A3KJ TCGA-DK-A1A3 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        5.46         2.53        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IS 
      130.88        17.62        15.62         7.79        87.32        50.27 
TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3N5 TCGA-FD-A3SJ TCGA-FJ-A3ZE TCGA-G2-A2EK 
       43.59         8.94        11.93        24.30         3.48         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3QF 
       35.24        17.26        15.91         7.73        11.31         7.63 
TCGA-GV-A3QH 
        7.79 

$`KDM6A WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.74        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 
        8.35        12.82         2.07        15.42        28.70         1.94 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YN 
        2.93        23.01         2.04         0.46         0.69        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1AD 
        4.90         7.20         5.19        16.31         2.14       112.44 
TCGA-DK-A1AE TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
       16.14         1.81        10.59       123.85         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        10.49        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 
        8.28        10.55       140.81        48.00        24.66         0.10 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SL 
       12.89         6.87         4.01        12.43        45.93        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
        1.97        15.19         4.08         3.25        22.32        61.94 
TCGA-G2-A2EJ TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       30.61         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP 
       15.81         4.50        14.07        17.75         1.12         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        3.12        20.98         4.41         6.41         6.15         5.69 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  KDM6A MUTATED KDM6A WILD-TYPE 
           0.43            0.10 
  KDM6A MUTATED KDM6A WILD-TYPE 
         130.88          140.81 
  KDM6A MUTATED KDM6A WILD-TYPE 
         11.310           8.315 
[1] "0.4 - 130.9 (11.3)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.1"
D2V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM6A MUTATED         0        7         7       16
  KDM6A WILD-TYPE       1       30        37       28
D2V3, multiclass
           clus
vv          KDM6A MUTATED KDM6A WILD-TYPE
  STAGE I               0               1
  STAGE II              7              30
  STAGE III             7              37
  STAGE IV             16              28
[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              T1+T2 T3 T4
  KDM6A MUTATED       8 17  2
  KDM6A WILD-TYPE    23 48 15
D2V4, multiclass
       clus
vv      KDM6A MUTATED KDM6A WILD-TYPE
  T1+T2             8              23
  T3               17              48
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  KDM6A MUTATED   13  6  7  2
  KDM6A WILD-TYPE 61  7 17  4
D2V5, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  N0            13              61
  N1             6               7
  N2             7              17
  N3             2               4
[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              M0 M1 MX
  KDM6A MUTATED   20  1 10
  KDM6A WILD-TYPE 56  3 39
D2V6, multiclass
    clus
vv   KDM6A MUTATED KDM6A WILD-TYPE
  M0            20              56
  M1             1               3
  MX            10              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"
D2V7, binary
                 cls
clus               0  1
  KDM6A MUTATED    9 22
  KDM6A WILD-TYPE 23 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM6A MUTATED      9   22
  KDM6A WILD-TYPE   23   76
        clus
vv       KDM6A MUTATED KDM6A WILD-TYPE
  FEMALE             9              23
  MALE              22              76
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
D2V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM6A MUTATED       1                         2    28
  KDM6A WILD-TYPE     7                         4    79
D2V11, multiclass
                           clus
vv                          KDM6A MUTATED KDM6A WILD-TYPE
  ASIAN                                 1               7
  BLACK OR AFRICAN AMERICAN             2               4
  WHITE                                28              79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RB1 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  RB1 MUTATED    8  9
  RB1 WILD-TYPE 72 36
  RB1 MUTATED RB1 WILD-TYPE 
           17           108 
  RB1 MUTATED RB1 WILD-TYPE 
            9            36 
$`RB1 MUTATED`
TCGA-BT-A20R TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-CU-A0YN TCGA-DK-A3IL 
        5.06         4.67        12.82         1.94        12.92         3.98 
TCGA-DK-A3IN TCGA-DK-A3IV TCGA-DK-A3X1 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3N5 
        8.22         9.67        48.00         6.87         4.01        11.93 
TCGA-FD-A3SL TCGA-FD-A3SO TCGA-GC-A3YS TCGA-GV-A3JX TCGA-GV-A40G 
       22.45         5.52         1.12         6.15        19.07 

$`RB1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PK TCGA-BT-A42B 
       14.96         8.35         5.59         3.65         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
       28.70         2.93        23.01         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
        0.69         4.90         7.20         5.46         5.19        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
      130.88       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM 
       10.59         7.79       123.85        87.32         2.20         7.82 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW TCGA-DK-A3WX 
       10.49        50.27        21.30        20.02         8.28        10.55 
TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
      140.81        43.59        24.66         0.10        12.89         8.94 
TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP 
       12.43        45.93        24.30         6.12        12.82        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       46.78        19.79         1.97        15.19         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25        22.32        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GD-A2C5 
       15.81         4.50        15.91        14.07        17.75         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  RB1 MUTATED RB1 WILD-TYPE 
         1.12          0.10 
  RB1 MUTATED RB1 WILD-TYPE 
        48.00        140.81 
  RB1 MUTATED RB1 WILD-TYPE 
        6.870         9.715 
[1] "1.1 - 48.0 (6.9)"  "0.1 - 140.8 (9.7)"
[1] "hr=" "2.1"
D3V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  RB1 MUTATED         0        5         6        6
  RB1 WILD-TYPE       1       32        38       38
D3V3, multiclass
           clus
vv          RB1 MUTATED RB1 WILD-TYPE
  STAGE I             0             1
  STAGE II            5            32
  STAGE III           6            38
  STAGE IV            6            38
[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            T1+T2 T3 T4
  RB1 MUTATED       4 10  2
  RB1 WILD-TYPE    27 55 15
D3V4, multiclass
       clus
vv      RB1 MUTATED RB1 WILD-TYPE
  T1+T2           4            27
  T3             10            55
  T4              2            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  RB1 MUTATED    9  3  3  1
  RB1 WILD-TYPE 65 10 21  5
D3V5, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  N0           9            65
  N1           3            10
  N2           3            21
  N3           1             5
[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            M0 M1 MX
  RB1 MUTATED    8  1  8
  RB1 WILD-TYPE 68  3 41
D3V6, multiclass
    clus
vv   RB1 MUTATED RB1 WILD-TYPE
  M0           8            68
  M1           1             3
  MX           8            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"
D3V7, binary
               cls
clus             0  1
  RB1 MUTATED    3 14
  RB1 WILD-TYPE 29 84
[1] "tbl2"
               cls
clus            [,1] [,2]
  RB1 MUTATED      3   14
  RB1 WILD-TYPE   29   84
        clus
vv       RB1 MUTATED RB1 WILD-TYPE
  FEMALE           3            29
  MALE            14            84
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
D3V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RB1 MUTATED       0                         2    14
  RB1 WILD-TYPE     8                         4    93
D3V11, multiclass
                           clus
vv                          RB1 MUTATED RB1 WILD-TYPE
  ASIAN                               0             8
  BLACK OR AFRICAN AMERICAN           2             4
  WHITE                              14            93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = ARID1A MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED   20 11
  ARID1A WILD-TYPE 60 34
  ARID1A MUTATED ARID1A WILD-TYPE 
              31               94 
  ARID1A MUTATED ARID1A WILD-TYPE 
              11               34 
$`ARID1A MUTATED`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20Q TCGA-BT-A20R 
       40.08         7.33         6.74        11.93        19.50         5.06 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-CF-A1HR TCGA-CU-A0YO TCGA-CU-A3KJ 
        3.65         4.67        12.82         0.46         4.90         5.46 
TCGA-DK-A1AD TCGA-DK-A2HX TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IU 
      112.44         1.81         2.20         7.82         8.22        20.02 
TCGA-FD-A3B3 TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FJ-A3ZF TCGA-G2-A2EK 
       12.89        12.82        13.18        19.79         4.08         5.69 
TCGA-GC-A3RC TCGA-GD-A2C5 TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3QK TCGA-H4-A2HO 
       15.91         7.73        11.31         4.41         6.67         1.51 
TCGA-K4-A3WV 
        4.67 

$`ARID1A WILD-TYPE`
TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P 
        2.66         6.58        19.04        32.84        12.16        17.88 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42B 
       14.89        14.96         8.35         5.59         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS 
       28.70         1.94         2.93        23.01         2.04         0.43 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        0.69        12.92         7.20         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       16.14        17.62        15.62        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV 
       87.32         3.98        10.49        50.27        21.30         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 
        8.28        10.55       140.81        48.00        43.59        24.66 
TCGA-E7-A3Y1 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
        0.10         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SQ 
       45.93        24.30        22.45         6.12         5.52        46.78 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
        1.97        15.19         3.48         3.25        22.32        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61        35.24        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC 
        2.89         2.24        15.81         4.50        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GV-A3JW TCGA-GV-A3JX 
        1.12         2.10         3.12        20.98         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         7.79         4.14         6.41        19.07 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.74        38.60         8.75         3.45 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.46             0.10 
  ARID1A MUTATED ARID1A WILD-TYPE 
          112.44           140.81 
  ARID1A MUTATED ARID1A WILD-TYPE 
            7.33            10.52 
[1] "0.5 - 112.4 (7.3)"  "0.1 - 140.8 (10.5)"
[1] "hr=" "1.3"
D4V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         1        6        11       13
  ARID1A WILD-TYPE       0       31        33       31
D4V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                1                0
  STAGE II               6               31
  STAGE III             11               33
  STAGE IV              13               31
[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               T1+T2 T3 T4
  ARID1A MUTATED       5 20  4
  ARID1A WILD-TYPE    26 45 13
D4V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1+T2              5               26
  T3                20               45
  T4                 4               13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ARID1A MUTATED   17  3  9  1
  ARID1A WILD-TYPE 57 10 15  5
D4V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0             17               57
  N1              3               10
  N2              9               15
  N3              1                5
[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               M0 M1 MX
  ARID1A MUTATED   21  0 11
  ARID1A WILD-TYPE 55  4 38
D4V6, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0             21               55
  M1              0                4
  MX             11               38
[1] 3 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
  ARID1A MUTATED    9 23
  ARID1A WILD-TYPE 23 75
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      9   23
  ARID1A WILD-TYPE   23   75
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              9               23
  MALE               23               75
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
D4V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       2                         0    29
  ARID1A WILD-TYPE     6                         6    78
D4V11, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  2                6
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                 29               78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = CDKN1A MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  CDKN1A MUTATED   10  6
  CDKN1A WILD-TYPE 70 39
  CDKN1A MUTATED CDKN1A WILD-TYPE 
              16              109 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
               6               39 
$`CDKN1A MUTATED`
TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A3QU TCGA-DK-A1AC 
       14.89        28.70         0.43         0.69         5.19       130.88 
TCGA-DK-A2HX TCGA-DK-A2I4 TCGA-DK-A3IN TCGA-FD-A3B7 TCGA-FD-A3SM TCGA-FD-A3SO 
        1.81       123.85         8.22         4.01         6.12         5.52 
TCGA-G2-A3IB TCGA-GD-A3OQ TCGA-GV-A3JX TCGA-GV-A40E 
        7.04         3.12         6.15         6.41 

$`CDKN1A WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
        2.07        15.42         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3YL 
        0.46        12.92         4.90         7.20         5.46        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62        15.62        10.59         7.79 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         3.98         7.82        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
       48.00        43.59        24.66         0.10        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87        12.43        11.93        45.93        24.30        22.45 
TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 
       12.82        13.18        46.78        19.79         1.97        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.48         4.08         3.25        22.32        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
        5.69        35.24        17.26        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV 
        1.12         7.73         2.10        20.98        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  CDKN1A MUTATED CDKN1A WILD-TYPE 
            0.43             0.10 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
          130.88           140.81 
  CDKN1A MUTATED CDKN1A WILD-TYPE 
           6.135           10.550 
[1] "0.4 - 130.9 (6.1)"  "0.1 - 140.8 (10.6)"
[1] "hr=" "1.4"
D5V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN1A MUTATED         0        4         6        6
  CDKN1A WILD-TYPE       1       33        38       38
D5V3, multiclass
           clus
vv          CDKN1A MUTATED CDKN1A WILD-TYPE
  STAGE I                0                1
  STAGE II               4               33
  STAGE III              6               38
  STAGE IV               6               38
[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               T1+T2 T3 T4
  CDKN1A MUTATED       2 11  2
  CDKN1A WILD-TYPE    29 54 15
D5V4, multiclass
       clus
vv      CDKN1A MUTATED CDKN1A WILD-TYPE
  T1+T2              2               29
  T3                11               54
  T4                 2               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDKN1A MUTATED   10  4  2  0
  CDKN1A WILD-TYPE 64  9 22  6
D5V5, multiclass
    clus
vv   CDKN1A MUTATED CDKN1A WILD-TYPE
  N0             10               64
  N1              4                9
  N2              2               22
  N3              0                6
[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               M0 M1 MX
  CDKN1A MUTATED   11  1  6
  CDKN1A WILD-TYPE 65  3 43
D5V6, multiclass
    clus
vv   CDKN1A MUTATED CDKN1A WILD-TYPE
  M0             11               65
  M1              1                3
  MX              6               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"
D5V7, binary
                  cls
clus                0  1
  CDKN1A MUTATED    2 16
  CDKN1A WILD-TYPE 30 82
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN1A MUTATED      2   16
  CDKN1A WILD-TYPE   30   82
        clus
vv       CDKN1A MUTATED CDKN1A WILD-TYPE
  FEMALE              2               30
  MALE               16               82
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
D5V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN1A MUTATED       4                         2    12
  CDKN1A WILD-TYPE     4                         4    95
D5V11, multiclass
                           clus
vv                          CDKN1A MUTATED CDKN1A WILD-TYPE
  ASIAN                                  4                4
  BLACK OR AFRICAN AMERICAN              2                4
  WHITE                                 12               95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MLL2 MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  MLL2 MUTATED   29  7
  MLL2 WILD-TYPE 51 38
  MLL2 MUTATED MLL2 WILD-TYPE 
            36             89 
  MLL2 MUTATED MLL2 WILD-TYPE 
             7             38 
$`MLL2 MUTATED`
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C 
       11.93        32.84        12.82         2.07        15.42        28.70 
TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CU-A3YL TCGA-DK-A1AC TCGA-DK-A1AD 
        2.93        23.01         2.04        16.31       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A2I1 TCGA-DK-A3IM TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3WW 
       16.14        10.59         7.82        21.30        20.02         8.28 
TCGA-DK-A3X1 TCGA-E7-A3Y1 TCGA-FD-A3B5 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP 
       48.00         0.10         8.94        22.45         6.12        13.18 
TCGA-G2-A2EF TCGA-G2-A3IB TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3RB TCGA-GC-A3RD 
       61.94         7.04         0.85         2.24         4.50        14.07 
TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GV-A3QI TCGA-GV-A40E TCGA-H4-A2HQ TCGA-K4-A3WS 
       17.75         2.10         4.14         6.41         6.74         8.75 

$`MLL2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         2.66         6.74         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-C4-A0F0 TCGA-CF-A1HR 
        8.35         5.59         3.65         4.67         1.94         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.43         0.69        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 
        8.91        17.62        15.62         1.81         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         3.98         8.22        10.49        50.27 
TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-FD-A3B3 
        9.67        10.55       140.81        43.59        24.66        12.89 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        45.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 
       12.82         5.52        46.78        19.79         1.97        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         4.08         3.25        22.32        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3OO TCGA-GC-A3RC 
       35.24        17.26        20.12         2.89        15.81        15.91 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV 
        1.12         7.73         3.12        20.98        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        6.41         6.15         5.69         7.63         7.79         6.67 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07         1.51        38.60         3.45         4.67 

  MLL2 MUTATED MLL2 WILD-TYPE 
          0.10           0.43 
  MLL2 MUTATED MLL2 WILD-TYPE 
        130.88         140.81 
  MLL2 MUTATED MLL2 WILD-TYPE 
         11.26           8.22 
[1] "0.1 - 130.9 (11.3)" "0.4 - 140.8 (8.2)" 
[1] "hr=" "2.5"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MLL2 MUTATED         0        9        19        8
  MLL2 WILD-TYPE       1       28        25       36
D6V3, multiclass
           clus
vv          MLL2 MUTATED MLL2 WILD-TYPE
  STAGE I              0              1
  STAGE II             9             28
  STAGE III           19             25
  STAGE IV             8             36
[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             T1+T2 T3 T4
  MLL2 MUTATED       4 21  4
  MLL2 WILD-TYPE    27 44 13
D6V4, multiclass
       clus
vv      MLL2 MUTATED MLL2 WILD-TYPE
  T1+T2            4             27
  T3              21             44
  T4               4             13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  MLL2 MUTATED   24  2  5  1
  MLL2 WILD-TYPE 50 11 19  5
D6V5, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  N0           24             50
  N1            2             11
  N2            5             19
  N3            1              5
[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             M0 M1 MX
  MLL2 MUTATED   21  3 11
  MLL2 WILD-TYPE 55  1 38
D6V6, multiclass
    clus
vv   MLL2 MUTATED MLL2 WILD-TYPE
  M0           21             55
  M1            3              1
  MX           11             38
[1] 3 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
  MLL2 MUTATED    8 28
  MLL2 WILD-TYPE 24 70
[1] "tbl2"
                cls
clus             [,1] [,2]
  MLL2 MUTATED      8   28
  MLL2 WILD-TYPE   24   70
        clus
vv       MLL2 MUTATED MLL2 WILD-TYPE
  FEMALE            8             24
  MALE             28             70
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
D6V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL2 MUTATED       1                         3    27
  MLL2 WILD-TYPE     7                         3    80
D6V11, multiclass
                           clus
vv                          MLL2 MUTATED MLL2 WILD-TYPE
  ASIAN                                1              7
  BLACK OR AFRICAN AMERICAN            3              3
  WHITE                               27             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = ELF3 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  ELF3 MUTATED    8  3
  ELF3 WILD-TYPE 72 42
  ELF3 MUTATED ELF3 WILD-TYPE 
            11            114 
  ELF3 MUTATED ELF3 WILD-TYPE 
             3             42 
$`ELF3 MUTATED`
TCGA-BT-A20Q TCGA-CF-A1HS TCGA-CU-A0YR TCGA-CU-A3YL TCGA-E5-A2PC TCGA-FD-A3SQ 
       19.50         0.43         7.20        16.31        43.59        46.78 
TCGA-FJ-A3ZF TCGA-G2-A2EO TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GV-A3JV 
        4.08        35.24         7.73         2.10         4.41 

$`ELF3 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20R TCGA-BT-A20T 
       19.04        32.84        12.16        17.88         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ 
        2.04         0.46         0.69        12.92         4.90         5.46 
TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.10        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 
       12.82         5.52        13.18        19.79         1.97        15.19 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
        3.12        20.98        11.31         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  ELF3 MUTATED ELF3 WILD-TYPE 
          0.43           0.10 
  ELF3 MUTATED ELF3 WILD-TYPE 
         46.78         140.81 
  ELF3 MUTATED ELF3 WILD-TYPE 
         7.730          8.925 
[1] "0.4 - 46.8 (7.7)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.5"
D7V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ELF3 MUTATED         0        0         3        7
  ELF3 WILD-TYPE       1       37        41       37
D7V3, multiclass
           clus
vv          ELF3 MUTATED ELF3 WILD-TYPE
  STAGE I              0              1
  STAGE II             0             37
  STAGE III            3             41
  STAGE IV             7             37
[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             T1+T2 T3 T4
  ELF3 MUTATED       2  6  2
  ELF3 WILD-TYPE    29 59 15
D7V4, multiclass
       clus
vv      ELF3 MUTATED ELF3 WILD-TYPE
  T1+T2            2             29
  T3               6             59
  T4               2             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ELF3 MUTATED    4  2  5  0
  ELF3 WILD-TYPE 70 11 19  6
D7V5, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  N0            4             70
  N1            2             11
  N2            5             19
  N3            0              6
[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             M0 M1 MX
  ELF3 MUTATED    6  0  5
  ELF3 WILD-TYPE 70  4 44
D7V6, multiclass
    clus
vv   ELF3 MUTATED ELF3 WILD-TYPE
  M0            6             70
  M1            0              4
  MX            5             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"
D7V7, binary
                cls
clus              0  1
  ELF3 MUTATED    4  7
  ELF3 WILD-TYPE 28 91
[1] "tbl2"
                cls
clus             [,1] [,2]
  ELF3 MUTATED      4    7
  ELF3 WILD-TYPE   28   91
        clus
vv       ELF3 MUTATED ELF3 WILD-TYPE
  FEMALE            4             28
  MALE              7             91
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
D7V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ELF3 MUTATED       1                         0    10
  ELF3 WILD-TYPE     7                         6    97
D7V11, multiclass
                           clus
vv                          ELF3 MUTATED ELF3 WILD-TYPE
  ASIAN                                1              7
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               10             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = FGFR3 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  FGFR3 MUTATED   13  3
  FGFR3 WILD-TYPE 67 42
  FGFR3 MUTATED FGFR3 WILD-TYPE 
             16             109 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              3              42 
$`FGFR3 MUTATED`
TCGA-BT-A0S7 TCGA-BT-A20T TCGA-BT-A42C TCGA-CF-A27C TCGA-DK-A1AG TCGA-DK-A3IS 
        6.58        14.89        28.70         0.69        15.62        50.27 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3SM TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       43.59        24.66         0.10         6.12         3.48         4.08 
TCGA-G2-A2EO TCGA-GC-A3BM TCGA-GU-A42R TCGA-H4-A2HQ 
       35.24         2.89        11.31         6.74 

$`FGFR3 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.74        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       32.84        12.16        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       15.42         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.43        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX 
        8.91       130.88       112.44        16.14        17.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        7.82         8.22        10.49        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-FD-A3B3 TCGA-FD-A3B5 
        8.28        10.55       140.81        48.00        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        1.97        15.19         3.25        22.32        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3I6 
        5.69        17.26         7.04        20.12         0.85         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.10         3.12        20.98         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41        19.07         1.51        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
           0.10            0.43 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          50.27          140.81 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          9.025           8.910 
[1] "0.1 - 50.3 (9.0)"  "0.4 - 140.8 (8.9)"
[1] "hr=" "2.2"
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FGFR3 MUTATED         0        6         4        5
  FGFR3 WILD-TYPE       1       31        40       39
D8V3, multiclass
           clus
vv          FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I               0               1
  STAGE II              6              31
  STAGE III             4              40
  STAGE IV              5              39
[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              T1+T2 T3 T4
  FGFR3 MUTATED       4  5  1
  FGFR3 WILD-TYPE    27 60 16
D8V4, multiclass
       clus
vv      FGFR3 MUTATED FGFR3 WILD-TYPE
  T1+T2             4              27
  T3                5              60
  T4                1              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FGFR3 MUTATED    9  2  1  1
  FGFR3 WILD-TYPE 65 11 23  5
D8V5, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  N0             9              65
  N1             2              11
  N2             1              23
  N3             1               5
[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              M0 M1 MX
  FGFR3 MUTATED   10  3  3
  FGFR3 WILD-TYPE 66  1 46
D8V6, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  M0            10              66
  M1             3               1
  MX             3              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
  FGFR3 MUTATED    2 14
  FGFR3 WILD-TYPE 30 84
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      2   14
  FGFR3 WILD-TYPE   30   84
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             2              30
  MALE              14              84
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
D8V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED       1                         1    14
  FGFR3 WILD-TYPE     7                         5    93
D8V11, multiclass
                           clus
vv                          FGFR3 MUTATED FGFR3 WILD-TYPE
  ASIAN                                 1               7
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                14              93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = CDKN2A MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  CDKN2A MUTATED    5  2
  CDKN2A WILD-TYPE 75 43
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               7              118 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2               43 
$`CDKN2A MUTATED`
TCGA-DK-A3X1 TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GD-A3OS 
       48.00        35.24        17.26         0.85         2.89        20.98 
TCGA-GV-A40E 
        6.41 

$`CDKN2A WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
       12.82         2.07        15.42        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN 
       23.01         2.04         0.46         0.43         0.69        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        4.90         7.20         5.46         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 
        8.28        10.55       140.81        43.59        24.66         0.10 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       13.18        46.78        19.79         1.97        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        7.04        20.12         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         1.12         7.73         2.10         3.12 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        7.79         4.14         6.67        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  CDKN2A MUTATED CDKN2A WILD-TYPE 
            0.85             0.10 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           48.00           140.81 
  CDKN2A MUTATED CDKN2A WILD-TYPE 
           17.26             8.83 
[1] "0.8 - 48.0 (17.3)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.6"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CDKN2A MUTATED         0        5         2        0
  CDKN2A WILD-TYPE       1       32        42       44
D9V3, multiclass
           clus
vv          CDKN2A MUTATED CDKN2A WILD-TYPE
  STAGE I                0                1
  STAGE II               5               32
  STAGE III              2               42
  STAGE IV               0               44
[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               T1+T2 T3 T4
  CDKN2A MUTATED       1  3  0
  CDKN2A WILD-TYPE    30 62 17
D9V4, multiclass
       clus
vv      CDKN2A MUTATED CDKN2A WILD-TYPE
  T1+T2              1               30
  T3                 3               62
  T4                 0               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CDKN2A MUTATED    4  0  0  0
  CDKN2A WILD-TYPE 70 13 24  6
D9V5, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  N0              4               70
  N1              0               13
  N2              0               24
  N3              0                6
[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               M0 M1 MX
  CDKN2A MUTATED    4  0  2
  CDKN2A WILD-TYPE 72  4 47
D9V6, multiclass
    clus
vv   CDKN2A MUTATED CDKN2A WILD-TYPE
  M0              4               72
  M1              0                4
  MX              2               47
[1] 3 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
  CDKN2A MUTATED    2  5
  CDKN2A WILD-TYPE 30 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CDKN2A MUTATED      2    5
  CDKN2A WILD-TYPE   30   93
        clus
vv       CDKN2A MUTATED CDKN2A WILD-TYPE
  FEMALE              2               30
  MALE                5               93
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
D9V10, continuous
[1] "Remove cluster labels:" "CDKN2A MUTATED"        
clus
  CDKN2A MUTATED CDKN2A WILD-TYPE 
               2               93 
      TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BL-A3JM 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-BT-A0S7       TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-BT-A20O       TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-BT-A20W       TCGA-BT-A2LB       TCGA-BT-A2LD       TCGA-BT-A3PH 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-BT-A3PJ       TCGA-BT-A3PK       TCGA-BT-A42B       TCGA-BT-A42C 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR       TCGA-CU-A3KJ 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-DK-A1A3       TCGA-DK-A1A5 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A1A6       TCGA-DK-A1A7       TCGA-DK-A1AA       TCGA-DK-A1AB 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A1AD       TCGA-DK-A1AE       TCGA-DK-A1AF 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A1AG       TCGA-DK-A2HX       TCGA-DK-A2I1       TCGA-DK-A2I2 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A2I4       TCGA-DK-A2I6       TCGA-DK-A3IK       TCGA-DK-A3IL 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A3IM       TCGA-DK-A3IN       TCGA-DK-A3IQ       TCGA-DK-A3IS 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A3IT       TCGA-DK-A3IU       TCGA-DK-A3WW       TCGA-DK-A3WX 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-DK-A3WY       TCGA-E5-A2PC       TCGA-FD-A3B3       TCGA-FD-A3B5 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-FD-A3B6       TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SL       TCGA-FD-A3SM 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-FD-A3SN       TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-FD-A3SR       TCGA-FD-A3SS       TCGA-FJ-A3Z7       TCGA-FT-A3EE 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RB       TCGA-GC-A3RC 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GD-A3OP       TCGA-GD-A3OQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QI 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40G       TCGA-H4-A2HO       TCGA-K4-A3WS 
"CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" "CDKN2A WILD-TYPE" 
      TCGA-K4-A3WV 
"CDKN2A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CDKN2A MUTATED       1                         0     6
  CDKN2A WILD-TYPE     7                         6   101
D9V11, multiclass
                           clus
vv                          CDKN2A MUTATED CDKN2A WILD-TYPE
  ASIAN                                  1                7
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  6              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = STAG2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  STAG2 MUTATED   10  3
  STAG2 WILD-TYPE 70 42
  STAG2 MUTATED STAG2 WILD-TYPE 
             13             112 
  STAG2 MUTATED STAG2 WILD-TYPE 
              3              42 
$`STAG2 MUTATED`
TCGA-BL-A13J TCGA-CF-A27C TCGA-DK-A1AA TCGA-DK-A1AF TCGA-DK-A3IS TCGA-E5-A2PC 
        2.66         0.69        19.00        17.62        50.27        43.59 
TCGA-E7-A3Y1 TCGA-FD-A3B5 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SQ TCGA-FJ-A3ZE 
        0.10         8.94        45.93        22.45        46.78         3.48 
TCGA-H4-A2HQ 
        6.74 

$`STAG2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         6.74         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       32.84        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        2.04         0.46         0.43        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         5.19        16.31         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AG 
       18.41         8.91       130.88       112.44        16.14        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT TCGA-DK-A3IU 
        3.98         7.82         8.22        10.49        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 
        9.67         8.28        10.55       140.81        48.00        24.66 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3SJ 
       12.89         6.87         4.01        12.43        11.93        24.30 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SR TCGA-FD-A3SS 
        6.12        12.82         5.52        13.18        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       15.19         4.08         3.25        22.32        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
        5.69        35.24        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         1.12         7.73         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        19.07         1.51 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  STAG2 MUTATED STAG2 WILD-TYPE 
           0.10            0.43 
  STAG2 MUTATED STAG2 WILD-TYPE 
          50.27          140.81 
  STAG2 MUTATED STAG2 WILD-TYPE 
          17.62            8.55 
[1] "0.1 - 50.3 (17.6)" "0.4 - 140.8 (8.6)"
[1] "hr=" "2.1"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  STAG2 MUTATED         0        4         1        8
  STAG2 WILD-TYPE       1       33        43       36
D10V3, multiclass
           clus
vv          STAG2 MUTATED STAG2 WILD-TYPE
  STAGE I               0               1
  STAGE II              4              33
  STAGE III             1              43
  STAGE IV              8              36
[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              T1+T2 T3 T4
  STAG2 MUTATED       5  4  2
  STAG2 WILD-TYPE    26 61 15
D10V4, multiclass
       clus
vv      STAG2 MUTATED STAG2 WILD-TYPE
  T1+T2             5              26
  T3                4              61
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  STAG2 MUTATED    6  2  4  1
  STAG2 WILD-TYPE 68 11 20  5
D10V5, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  N0             6              68
  N1             2              11
  N2             4              20
  N3             1               5
[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              M0 M1 MX
  STAG2 MUTATED    7  3  4
  STAG2 WILD-TYPE 69  1 45
D10V6, multiclass
    clus
vv   STAG2 MUTATED STAG2 WILD-TYPE
  M0             7              69
  M1             3               1
  MX             4              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
  STAG2 MUTATED    3 11
  STAG2 WILD-TYPE 29 87
[1] "tbl2"
                 cls
clus              [,1] [,2]
  STAG2 MUTATED      3   11
  STAG2 WILD-TYPE   29   87
        clus
vv       STAG2 MUTATED STAG2 WILD-TYPE
  FEMALE             3              29
  MALE              11              87
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
D10V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  STAG2 MUTATED       2                         2    10
  STAG2 WILD-TYPE     6                         4    97
D10V11, multiclass
                           clus
vv                          STAG2 MUTATED STAG2 WILD-TYPE
  ASIAN                                 2               6
  BLACK OR AFRICAN AMERICAN             2               4
  WHITE                                10              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = NFE2L2 MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED    7  4
  NFE2L2 WILD-TYPE 73 41
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
              11              114 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               41 
$`NFE2L2 MUTATED`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20U TCGA-BT-A42B TCGA-C4-A0F6 TCGA-DK-A1AE 
        7.33        11.93        14.96        15.42        23.01        16.14 
TCGA-DK-A3IT TCGA-E5-A2PC TCGA-FD-A3SM TCGA-G2-A3IB TCGA-K4-A3WS 
       21.30        43.59         6.12         7.04         8.75 

$`NFE2L2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66         6.74         6.58        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W 
       12.16        17.88        19.50         5.06        14.89         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42C 
        5.59         3.65         4.67        12.82         2.07        28.70 
TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
        1.94         2.93         2.04         0.46         0.43         0.69 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL 
       12.92         4.90         7.20         5.46         5.19        16.31 
TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB 
        2.53         2.14        66.41        18.41        19.00         8.91 
TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      130.88       112.44        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW 
        8.22        10.49        50.27        20.02         9.67         8.28 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
       10.55       140.81        48.00        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       19.79         1.97        15.19         3.48         4.08         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
       22.32        61.94        30.61         5.69        35.24        17.26 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12        20.98        11.31         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV 
       19.07         1.51         6.74        38.60         3.45         4.67 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
            6.12             0.10 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           43.59           140.81 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          14.960            8.315 
[1] "6.1 - 43.6 (15.0)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.2"
D11V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  NFE2L2 MUTATED         0        1         7        3
  NFE2L2 WILD-TYPE       1       36        37       41
D11V3, multiclass
           clus
vv          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  STAGE I                0                1
  STAGE II               1               36
  STAGE III              7               37
  STAGE IV               3               41
[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               T1+T2 T3 T4
  NFE2L2 MUTATED       1  9  0
  NFE2L2 WILD-TYPE    30 56 17
D11V4, multiclass
       clus
vv      NFE2L2 MUTATED NFE2L2 WILD-TYPE
  T1+T2              1               30
  T3                 9               56
  T4                 0               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  NFE2L2 MUTATED    7  2  1  0
  NFE2L2 WILD-TYPE 67 11 23  6
D11V5, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              7               67
  N1              2               11
  N2              1               23
  N3              0                6
[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               M0 M1 MX
  NFE2L2 MUTATED    6  1  4
  NFE2L2 WILD-TYPE 70  3 45
D11V6, multiclass
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  M0              6               70
  M1              1                3
  MX              4               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"
D11V7, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    5  6
  NFE2L2 WILD-TYPE 27 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      5    6
  NFE2L2 WILD-TYPE   27   92
        clus
vv       NFE2L2 MUTATED NFE2L2 WILD-TYPE
  FEMALE              5               27
  MALE                6               92
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2               35 
      TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-DK-A2HX       TCGA-DK-A3IN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DK-A3IV       TCGA-DK-A3WX       TCGA-G2-A2EC       TCGA-G2-A2EF 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EO       TCGA-G2-A2ES 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-G2-A3IE       TCGA-G2-A3VY       TCGA-GC-A3BM       TCGA-GC-A3I6 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD       TCGA-GC-A3YS 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-GD-A3OS       TCGA-GV-A3JV       TCGA-GV-A3JW       TCGA-GV-A3JX 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
D11V9, continuous
D11V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFE2L2 MUTATED       0                         1     8
  NFE2L2 WILD-TYPE     8                         5    99
D11V11, multiclass
                           clus
vv                          NFE2L2 MUTATED NFE2L2 WILD-TYPE
  ASIAN                                  0                8
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                  8               99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = ERCC2 MUTATION ANALYSIS
D12V1, survival
                 sevent
clus2              0  1
  ERCC2 MUTATED   11  5
  ERCC2 WILD-TYPE 69 40
  ERCC2 MUTATED ERCC2 WILD-TYPE 
             16             109 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
              5              40 
$`ERCC2 MUTATED`
TCGA-BT-A20O TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-CU-A0YR TCGA-DK-A1A3 TCGA-DK-A1A7 
       12.16        12.82         2.07         7.20         2.53        18.41 
TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-E5-A2PC TCGA-FD-A3N5 TCGA-FD-A3SN TCGA-FT-A3EE 
      130.88        87.32        43.59        11.93        12.82         3.25 
TCGA-G2-A2ES TCGA-GC-A3RC TCGA-GD-A3OQ TCGA-H4-A2HO 
       17.26        15.91         3.12         1.51 

$`ERCC2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        32.84        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A42B 
       14.96         8.35         5.59         3.65         4.67        15.42 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       28.70         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.43         0.69        12.92         4.90         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
       16.31         2.14        66.41        19.00         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
      123.85         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
      140.81        48.00        24.66         0.10        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        6.87         4.01        12.43        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
        6.12         5.52        13.18        46.78        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
       15.19         3.48         4.08        22.32        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
        5.69        35.24         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
        2.24        15.81         4.50        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        7.73         2.10        20.98        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
        6.41        19.07         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  ERCC2 MUTATED ERCC2 WILD-TYPE 
           1.51            0.10 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
         130.88          140.81 
  ERCC2 MUTATED ERCC2 WILD-TYPE 
          12.49            8.35 
[1] "1.5 - 130.9 (12.5)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.3"
D12V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERCC2 MUTATED         0        4         5        7
  ERCC2 WILD-TYPE       1       33        39       37
D12V3, multiclass
           clus
vv          ERCC2 MUTATED ERCC2 WILD-TYPE
  STAGE I               0               1
  STAGE II              4              33
  STAGE III             5              39
  STAGE IV              7              37
[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              T1+T2 T3 T4
  ERCC2 MUTATED       6  7  3
  ERCC2 WILD-TYPE    25 58 14
D12V4, multiclass
       clus
vv      ERCC2 MUTATED ERCC2 WILD-TYPE
  T1+T2             6              25
  T3                7              58
  T4                3              14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERCC2 MUTATED    9  3  3  1
  ERCC2 WILD-TYPE 65 10 21  5
D12V5, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  N0             9              65
  N1             3              10
  N2             3              21
  N3             1               5
[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              M0 M1 MX
  ERCC2 MUTATED    8  0  8
  ERCC2 WILD-TYPE 68  4 41
D12V6, multiclass
    clus
vv   ERCC2 MUTATED ERCC2 WILD-TYPE
  M0             8              68
  M1             0               4
  MX             8              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"
D12V7, binary
                 cls
clus               0  1
  ERCC2 MUTATED    3 13
  ERCC2 WILD-TYPE 29 85
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERCC2 MUTATED      3   13
  ERCC2 WILD-TYPE   29   85
        clus
vv       ERCC2 MUTATED ERCC2 WILD-TYPE
  FEMALE             3              29
  MALE              13              85
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
D12V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERCC2 MUTATED       0                         1    15
  ERCC2 WILD-TYPE     8                         5    92
D12V11, multiclass
                           clus
vv                          ERCC2 MUTATED ERCC2 WILD-TYPE
  ASIAN                                 0               8
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                15              92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = FBXW7 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    6  7
  FBXW7 WILD-TYPE 74 38
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             13             112 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              7              38 
$`FBXW7 MUTATED`
TCGA-BL-A13I TCGA-BT-A0YX TCGA-BT-A20O TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CU-A0YR 
        7.33        11.93        12.16         1.94         2.93         7.20 
TCGA-DK-A1AC TCGA-DK-A2I2 TCGA-DK-A3IN TCGA-DK-A3WX TCGA-G2-A2ES TCGA-GC-A3RD 
      130.88         7.79         8.22        10.55        17.26        14.07 
TCGA-K4-A3WU 
        3.45 

$`FBXW7 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         2.66         6.74         6.58        19.04        32.84 
TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W 
       17.88        19.50         5.06        14.89        14.96         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.70        23.01         2.04         0.46         0.43         0.69 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
       12.92         4.90         5.46         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD 
        2.14        66.41        18.41        19.00         8.91       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I4 
       16.14        17.62        15.62         1.81        10.59       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         3.98         7.82        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WY TCGA-DK-A3X1 
       21.30        20.02         9.67         8.28       140.81        48.00 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       43.59        24.66         0.10        12.89         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC 
        1.97        15.19         3.48         4.08         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A3IB TCGA-G2-A3IE 
       61.94        30.61         5.69        35.24         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         1.12         7.73         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WV 
        6.74        38.60         8.75         4.67 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.94            0.10 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         130.88          140.81 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          8.220           8.925 
[1] "1.9 - 130.9 (8.2)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.9"
D13V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FBXW7 MUTATED         0        2         9        2
  FBXW7 WILD-TYPE       1       35        35       42
D13V3, multiclass
           clus
vv          FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I               0               1
  STAGE II              2              35
  STAGE III             9              35
  STAGE IV              2              42
[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              T1+T2 T3 T4
  FBXW7 MUTATED       2  9  2
  FBXW7 WILD-TYPE    29 56 15
D13V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T1+T2             2              29
  T3                9              56
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FBXW7 MUTATED   11  0  1  1
  FBXW7 WILD-TYPE 63 13 23  5
D13V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0            11              63
  N1             0              13
  N2             1              23
  N3             1               5
[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              M0 M1 MX
  FBXW7 MUTATED   11  0  2
  FBXW7 WILD-TYPE 65  4 47
D13V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  M0            11              65
  M1             0               4
  MX             2              47
[1] 3 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
  FBXW7 MUTATED    5  8
  FBXW7 WILD-TYPE 27 90
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      5    8
  FBXW7 WILD-TYPE   27   90
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             5              27
  MALE               8              90
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
D13V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FBXW7 MUTATED       0                         0    10
  FBXW7 WILD-TYPE     8                         6    97
D13V11, multiclass
                           clus
vv                          FBXW7 MUTATED FBXW7 WILD-TYPE
  ASIAN                                 0               8
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                10              97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = RHOB MUTATION ANALYSIS
D14V1, survival
                sevent
clus2             0  1
  RHOB MUTATED    5  2
  RHOB WILD-TYPE 75 43
  RHOB MUTATED RHOB WILD-TYPE 
             7            118 
  RHOB MUTATED RHOB WILD-TYPE 
             2             43 
$`RHOB MUTATED`
TCGA-BT-A20N TCGA-BT-A3PJ TCGA-DK-A3IL TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-FD-A3SL 
       32.84        12.82         3.98        48.00        43.59        22.45 
TCGA-FJ-A3ZF 
        4.08 

$`RHOB WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        12.16        17.88        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK 
       14.96         8.35         5.59         3.65         4.67         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       15.42        28.70         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.46         0.43         0.69        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         5.19        16.31         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
       87.32         2.20         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.10        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SM TCGA-FD-A3SN 
       12.43        11.93        45.93        24.30         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 
        5.52        13.18        46.78        19.79         1.97        15.19 
TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        3.48         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         7.73         2.10         3.12        20.98        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  RHOB MUTATED RHOB WILD-TYPE 
          3.98           0.10 
  RHOB MUTATED RHOB WILD-TYPE 
         48.00         140.81 
  RHOB MUTATED RHOB WILD-TYPE 
         22.45           8.55 
[1] "4.0 - 48.0 (22.4)" "0.1 - 140.8 (8.6)"
[1] "hr=" "2"  
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RHOB MUTATED         0        0         4        3
  RHOB WILD-TYPE       1       37        40       41
D14V3, multiclass
           clus
vv          RHOB MUTATED RHOB WILD-TYPE
  STAGE I              0              1
  STAGE II             0             37
  STAGE III            4             40
  STAGE IV             3             41
[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             T1+T2 T3 T4
  RHOB MUTATED       1  4  1
  RHOB WILD-TYPE    30 61 16
D14V4, multiclass
       clus
vv      RHOB MUTATED RHOB WILD-TYPE
  T1+T2            1             30
  T3               4             61
  T4               1             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RHOB MUTATED    3  1  2  1
  RHOB WILD-TYPE 71 12 22  5
D14V5, multiclass
    clus
vv   RHOB MUTATED RHOB WILD-TYPE
  N0            3             71
  N1            1             12
  N2            2             22
  N3            1              5
[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             M0 M1 MX
  RHOB MUTATED    4  1  2
  RHOB WILD-TYPE 72  3 47
D14V6, multiclass
    clus
vv   RHOB MUTATED RHOB WILD-TYPE
  M0            4             72
  M1            1              3
  MX            2             47
[1] 3 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
  RHOB MUTATED    3  4
  RHOB WILD-TYPE 29 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  RHOB MUTATED      3    4
  RHOB WILD-TYPE   29   94
        clus
vv       RHOB MUTATED RHOB WILD-TYPE
  FEMALE            3             29
  MALE              4             94
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "RHOB MUTATED"          
clus
  RHOB MUTATED RHOB WILD-TYPE 
             1             36 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-DK-A2HX     TCGA-DK-A3IN 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-DK-A3IV     TCGA-DK-A3WX     TCGA-G2-A2EC     TCGA-G2-A2EF 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EO     TCGA-G2-A2ES 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GC-A3YS     TCGA-GD-A3OS     TCGA-GV-A3JV     TCGA-GV-A3JW 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GV-A3JX     TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
    TCGA-GV-A3QI     TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G 
"RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" "RHOB WILD-TYPE" 
D14V9, continuous
D14V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RHOB MUTATED       0                         0     6
  RHOB WILD-TYPE     8                         6   101
D14V11, multiclass
                           clus
vv                          RHOB MUTATED RHOB WILD-TYPE
  ASIAN                                0              8
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                6            101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = TSC1 MUTATION ANALYSIS
D15V1, survival
                sevent
clus2             0  1
  TSC1 MUTATED    7  3
  TSC1 WILD-TYPE 73 42
  TSC1 MUTATED TSC1 WILD-TYPE 
            10            115 
  TSC1 MUTATED TSC1 WILD-TYPE 
             3             42 
$`TSC1 MUTATED`
TCGA-BT-A20P TCGA-BT-A42C TCGA-CF-A1HR TCGA-DK-A1A3 TCGA-DK-A3WW TCGA-FD-A3SM 
       17.88        28.70         0.46         2.53         8.28         6.12 
TCGA-FD-A3SN TCGA-G2-A2EO TCGA-GD-A2C5 TCGA-GV-A3QF 
       12.82        35.24         7.73         7.63 

$`TSC1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T 
       19.04        32.84        12.16        19.50         5.06        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
        2.07        15.42         1.94         2.93        23.01         2.04 
TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ 
        0.43         0.69        12.92         4.90         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.19        16.31         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC 
       20.02         9.67        10.55       140.81        48.00        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.10        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO 
       12.43        11.93        45.93        24.30        22.45         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       13.18        46.78        19.79         1.97        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  TSC1 MUTATED TSC1 WILD-TYPE 
          0.46           0.10 
  TSC1 MUTATED TSC1 WILD-TYPE 
         35.24         140.81 
  TSC1 MUTATED TSC1 WILD-TYPE 
         8.005          8.940 
[1] "0.5 - 35.2 (8.0)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D15V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TSC1 MUTATED         0        2         3        5
  TSC1 WILD-TYPE       1       35        41       39
D15V3, multiclass
           clus
vv          TSC1 MUTATED TSC1 WILD-TYPE
  STAGE I              0              1
  STAGE II             2             35
  STAGE III            3             41
  STAGE IV             5             39
[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             T1+T2 T3 T4
  TSC1 MUTATED       1  9  0
  TSC1 WILD-TYPE    30 56 17
D15V4, multiclass
       clus
vv      TSC1 MUTATED TSC1 WILD-TYPE
  T1+T2            1             30
  T3               9             56
  T4               0             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  TSC1 MUTATED    7  0  4  0
  TSC1 WILD-TYPE 67 13 20  6
D15V5, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  N0            7             67
  N1            0             13
  N2            4             20
  N3            0              6
[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             M0 M1 MX
  TSC1 MUTATED    7  1  3
  TSC1 WILD-TYPE 69  3 46
D15V6, multiclass
    clus
vv   TSC1 MUTATED TSC1 WILD-TYPE
  M0            7             69
  M1            1              3
  MX            3             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"
D15V7, binary
                cls
clus              0  1
  TSC1 MUTATED    2  9
  TSC1 WILD-TYPE 30 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  TSC1 MUTATED      2    9
  TSC1 WILD-TYPE   30   89
        clus
vv       TSC1 MUTATED TSC1 WILD-TYPE
  FEMALE            2             30
  MALE              9             89
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
D15V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TSC1 MUTATED       2                         0     9
  TSC1 WILD-TYPE     6                         6    98
D15V11, multiclass
                           clus
vv                          TSC1 MUTATED TSC1 WILD-TYPE
  ASIAN                                2              6
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                9             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = FOXQ1 MUTATION ANALYSIS
D16V1, survival
                 sevent
clus2              0  1
  FOXQ1 MUTATED    7  0
  FOXQ1 WILD-TYPE 73 45
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              7             118 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              0              45 
$`FOXQ1 MUTATED`
TCGA-CF-A1HR TCGA-CU-A3YL TCGA-DK-A2I4 TCGA-DK-A3IM TCGA-DK-A3X1 TCGA-G2-A2EF 
        0.46        16.31       123.85         7.82        48.00        61.94 
TCGA-GC-A3RB 
        4.50 

$`FOXQ1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
       12.82         2.07        15.42        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
       23.01         2.04         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20         5.46         5.19         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 
       17.62        15.62         1.81        10.59         7.79        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         3.98         8.22        10.49        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC 
       20.02         9.67         8.28        10.55       140.81        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.10        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ 
       15.19         3.48         4.08         3.25        22.32        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
        5.69        35.24        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.89         2.24        15.81        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         7.73         2.10         3.12        20.98        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
           0.46            0.10 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
         123.85          140.81 
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
          16.31            8.83 
[1] "0.5 - 123.8 (16.3)" "0.1 - 140.8 (8.8)" 
[1] "hr="     "7.9e+07"
D16V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FOXQ1 MUTATED         0        1         5        0
  FOXQ1 WILD-TYPE       1       36        39       44
D16V3, multiclass
           clus
vv          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  STAGE I               0               1
  STAGE II              1              36
  STAGE III             5              39
  STAGE IV              0              44
[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              T1+T2 T3 T4
  FOXQ1 MUTATED       0  5  1
  FOXQ1 WILD-TYPE    31 60 16
D16V4, multiclass
       clus
vv      FOXQ1 MUTATED FOXQ1 WILD-TYPE
  T1+T2             0              31
  T3                5              60
  T4                1              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOXQ1 MUTATED    7  0  0  0
  FOXQ1 WILD-TYPE 67 13 24  6
D16V5, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  N0             7              67
  N1             0              13
  N2             0              24
  N3             0               6
[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              M0 M1 MX
  FOXQ1 MUTATED    7  0  0
  FOXQ1 WILD-TYPE 69  4 49
D16V6, multiclass
    clus
vv   FOXQ1 MUTATED FOXQ1 WILD-TYPE
  M0             7              69
  M1             0               4
  MX             0              49
[1] 3 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
  FOXQ1 MUTATED    1  6
  FOXQ1 WILD-TYPE 31 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXQ1 MUTATED      1    6
  FOXQ1 WILD-TYPE   31   92
        clus
vv       FOXQ1 MUTATED FOXQ1 WILD-TYPE
  FEMALE             1              31
  MALE               6              92
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "FOXQ1 MUTATED"         
clus
  FOXQ1 MUTATED FOXQ1 WILD-TYPE 
              1              36 
     TCGA-CF-A1HS      TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-DK-A2HX      TCGA-DK-A3IN 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-DK-A3IV      TCGA-DK-A3WX      TCGA-E5-A2PC      TCGA-G2-A2EC 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EO      TCGA-G2-A2ES 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY      TCGA-GC-A3BM 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GD-A3OS      TCGA-GV-A3JV      TCGA-GV-A3JW 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" "FOXQ1 WILD-TYPE" 
D16V9, continuous
D16V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXQ1 MUTATED       1                         0     6
  FOXQ1 WILD-TYPE     7                         6   101
D16V11, multiclass
                           clus
vv                          FOXQ1 MUTATED FOXQ1 WILD-TYPE
  ASIAN                                 1               7
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 6             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = PIK3CA MUTATION ANALYSIS
D17V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   20  6
  PIK3CA WILD-TYPE 60 39
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26               99 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               6               39 
$`PIK3CA MUTATED`
TCGA-BT-A20O TCGA-BT-A20R TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1AB TCGA-DK-A1AC 
       12.16         5.06         2.14        66.41         8.91       130.88 
TCGA-DK-A1AG TCGA-DK-A3WW TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-FD-A3B5 TCGA-FD-A3B6 
       15.62         8.28        48.00        43.59         8.94         6.87 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FD-A3SO TCGA-G2-A2EJ TCGA-G2-A2EO 
       45.93        24.30        12.82         5.52        30.61        35.24 
TCGA-G2-A3VY TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3WC TCGA-GD-A3OP TCGA-GV-A3JX 
        0.85         2.24        15.81        17.75         2.10         6.15 
TCGA-H4-A2HO TCGA-K4-A3WS 
        1.51         8.75 

$`PIK3CA WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       19.04        32.84        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       15.42        28.70         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.46         0.43         0.69        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A7 TCGA-DK-A1AA 
        5.46         5.19        16.31         2.53        18.41        19.00 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
      112.44        16.14        17.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WX 
       10.49        50.27        21.30        20.02         9.67        10.55 
TCGA-DK-A3WY TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B7 TCGA-FD-A3B8 
      140.81        24.66         0.10        12.89         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       11.93        22.45         6.12        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC 
        1.97        15.19         3.48         4.08         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM 
       61.94         5.69        17.26         7.04        20.12         2.89 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OQ 
        4.50        15.91        14.07         1.12         7.73         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JZ TCGA-GV-A3QF 
       20.98        11.31         4.41         6.41         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HQ 
        7.79         4.14         6.67         6.41        19.07         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         3.45         4.67 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.85             0.10 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          130.88           140.81 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           10.55             8.22 
[1] "0.8 - 130.9 (10.6)" "0.1 - 140.8 (8.2)" 
[1] "hr=" "2.1"
D17V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         0        6        11        9
  PIK3CA WILD-TYPE       1       31        33       35
D17V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                0                1
  STAGE II               6               31
  STAGE III             11               33
  STAGE IV               9               35
[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               T1+T2 T3 T4
  PIK3CA MUTATED       8 13  3
  PIK3CA WILD-TYPE    23 52 14
D17V4, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T1+T2              8               23
  T3                13               52
  T4                 3               14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  PIK3CA MUTATED   17  5  2  0
  PIK3CA WILD-TYPE 57  8 22  6
D17V5, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0             17               57
  N1              5                8
  N2              2               22
  N3              0                6
[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               M0 M1 MX
  PIK3CA MUTATED   12  0 13
  PIK3CA WILD-TYPE 64  4 36
D17V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0             12               64
  M1              0                4
  MX             13               36
[1] 3 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
  PIK3CA MUTATED    7 19
  PIK3CA WILD-TYPE 25 79
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7   19
  PIK3CA WILD-TYPE   25   79
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              7               25
  MALE               19               79
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
D17V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       1                         1    23
  PIK3CA WILD-TYPE     7                         5    84
D17V11, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  1                7
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                 23               84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = RXRA MUTATION ANALYSIS
D18V1, survival
                sevent
clus2             0  1
  RXRA MUTATED    7  5
  RXRA WILD-TYPE 73 40
  RXRA MUTATED RXRA WILD-TYPE 
            12            113 
  RXRA MUTATED RXRA WILD-TYPE 
             5             40 
$`RXRA MUTATED`
TCGA-BT-A3PH TCGA-DK-A1AC TCGA-DK-A1AF TCGA-DK-A3IL TCGA-DK-A3IQ TCGA-FD-A3B5 
        4.67       130.88        17.62         3.98        10.49         8.94 
TCGA-FD-A3SN TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-GV-A3QH TCGA-GV-A40G TCGA-H4-A2HQ 
       12.82         4.08        61.94         7.79        19.07         6.74 

$`RXRA WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ 
       14.89        14.96         8.35         5.59         3.65        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.04         0.46         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46         5.19        16.31         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       112.44        16.14 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         7.82         8.22        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC 
        9.67         8.28        10.55       140.81        48.00        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
       24.66         0.10        12.89         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO 
       11.93        45.93        24.30        22.45         6.12         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       13.18        46.78        19.79         1.97        15.19         3.48 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
        3.25        22.32        30.61         5.69        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04        20.12         0.85         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        4.50        15.91        14.07        17.75         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        6.15         5.69         7.63         4.14         6.67         6.41 
TCGA-H4-A2HO TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51        38.60         8.75         3.45         4.67 

  RXRA MUTATED RXRA WILD-TYPE 
          3.98           0.10 
  RXRA MUTATED RXRA WILD-TYPE 
        130.88         140.81 
  RXRA MUTATED RXRA WILD-TYPE 
         9.715          8.750 
[1] "4.0 - 130.9 (9.7)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D18V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RXRA MUTATED         0        3         3        6
  RXRA WILD-TYPE       1       34        41       38
D18V3, multiclass
           clus
vv          RXRA MUTATED RXRA WILD-TYPE
  STAGE I              0              1
  STAGE II             3             34
  STAGE III            3             41
  STAGE IV             6             38
[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             T1+T2 T3 T4
  RXRA MUTATED       2  6  0
  RXRA WILD-TYPE    29 59 17
D18V4, multiclass
       clus
vv      RXRA MUTATED RXRA WILD-TYPE
  T1+T2            2             29
  T3               6             59
  T4               0             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  RXRA MUTATED    6  1  3  0
  RXRA WILD-TYPE 68 12 21  6
D18V5, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  N0            6             68
  N1            1             12
  N2            3             21
  N3            0              6
[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             M0 M1 MX
  RXRA MUTATED    6  1  5
  RXRA WILD-TYPE 70  3 44
D18V6, multiclass
    clus
vv   RXRA MUTATED RXRA WILD-TYPE
  M0            6             70
  M1            1              3
  MX            5             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
  RXRA MUTATED    3  9
  RXRA WILD-TYPE 29 89
[1] "tbl2"
                cls
clus             [,1] [,2]
  RXRA MUTATED      3    9
  RXRA WILD-TYPE   29   89
        clus
vv       RXRA MUTATED RXRA WILD-TYPE
  FEMALE            3             29
  MALE              9             89
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
D18V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RXRA MUTATED       0                         2    10
  RXRA WILD-TYPE     8                         4    97
D18V11, multiclass
                           clus
vv                          RXRA MUTATED RXRA WILD-TYPE
  ASIAN                                0              8
  BLACK OR AFRICAN AMERICAN            2              4
  WHITE                               10             97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = CREBBP MUTATION ANALYSIS
D19V1, survival
                  sevent
clus2               0  1
  CREBBP MUTATED   12  4
  CREBBP WILD-TYPE 68 41
  CREBBP MUTATED CREBBP WILD-TYPE 
              16              109 
  CREBBP MUTATED CREBBP WILD-TYPE 
               4               41 
$`CREBBP MUTATED`
TCGA-BT-A20O TCGA-BT-A20T TCGA-BT-A3PJ TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-CU-A3YL 
       12.16        14.89        12.82         1.94         2.93        16.31 
TCGA-DK-A1A3 TCGA-DK-A1AD TCGA-DK-A2I1 TCGA-FD-A3N5 TCGA-FD-A3SL TCGA-FD-A3SM 
        2.53       112.44        10.59        11.93        22.45         6.12 
TCGA-FD-A3SP TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GV-A3JX 
       13.18        15.91        14.07         6.15 

$`CREBBP WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U 
       19.04        32.84        17.88        19.50         5.06        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         5.59         3.65         4.67         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C 
       28.70        23.01         2.04         0.46         0.43         0.69 
TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A5 
       12.92         4.90         7.20         5.46         5.19         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       130.88        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62        15.62         1.81         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
       48.00        43.59        24.66         0.10        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SN 
        6.87         4.01        12.43        45.93        24.30        12.82 
TCGA-FD-A3SO TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        5.52        46.78        19.79         1.97        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
        2.24        15.81         4.50        17.75         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  CREBBP MUTATED CREBBP WILD-TYPE 
            1.94             0.10 
  CREBBP MUTATED CREBBP WILD-TYPE 
          112.44           140.81 
  CREBBP MUTATED CREBBP WILD-TYPE 
           12.49             8.28 
[1] "1.9 - 112.4 (12.5)" "0.1 - 140.8 (8.3)" 
[1] "hr=" "1.5"
D19V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CREBBP MUTATED         0        4         7        6
  CREBBP WILD-TYPE       1       33        37       38
D19V3, multiclass
           clus
vv          CREBBP MUTATED CREBBP WILD-TYPE
  STAGE I                0                1
  STAGE II               4               33
  STAGE III              7               37
  STAGE IV               6               38
[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               T1+T2 T3 T4
  CREBBP MUTATED       4 11  2
  CREBBP WILD-TYPE    27 54 15
D19V4, multiclass
       clus
vv      CREBBP MUTATED CREBBP WILD-TYPE
  T1+T2              4               27
  T3                11               54
  T4                 2               15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CREBBP MUTATED   10  1  4  2
  CREBBP WILD-TYPE 64 12 20  4
D19V5, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  N0             10               64
  N1              1               12
  N2              4               20
  N3              2                4
[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               M0 M1 MX
  CREBBP MUTATED   10  2  5
  CREBBP WILD-TYPE 66  2 44
D19V6, multiclass
    clus
vv   CREBBP MUTATED CREBBP WILD-TYPE
  M0             10               66
  M1              2                2
  MX              5               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"
D19V7, binary
                  cls
clus                0  1
  CREBBP MUTATED    2 15
  CREBBP WILD-TYPE 30 83
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CREBBP MUTATED      2   15
  CREBBP WILD-TYPE   30   83
        clus
vv       CREBBP MUTATED CREBBP WILD-TYPE
  FEMALE              2               30
  MALE               15               83
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
D19V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CREBBP MUTATED       0                         1    14
  CREBBP WILD-TYPE     8                         5    93
D19V11, multiclass
                           clus
vv                          CREBBP MUTATED CREBBP WILD-TYPE
  ASIAN                                  0                8
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                 14               93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = ERBB3 MUTATION ANALYSIS
D20V1, survival
                 sevent
clus2              0  1
  ERBB3 MUTATED   10  4
  ERBB3 WILD-TYPE 70 41
  ERBB3 MUTATED ERBB3 WILD-TYPE 
             14             111 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
              4              41 
$`ERBB3 MUTATED`
TCGA-BT-A20R TCGA-DK-A1AA TCGA-DK-A1AG TCGA-DK-A3IL TCGA-DK-A3IN TCGA-FD-A3B6 
        5.06        19.00        15.62         3.98         8.22         6.87 
TCGA-FD-A3SJ TCGA-FD-A3SN TCGA-FJ-A3ZF TCGA-G2-A2EF TCGA-G2-A2EO TCGA-GD-A3OQ 
       24.30        12.82         4.08        61.94        35.24         3.12 
TCGA-GU-A42R TCGA-HQ-A2OE 
       11.31        38.60 

$`ERBB3 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T 
       19.04        32.84        12.16        17.88        19.50        14.89 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.96         8.35         5.59         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.04         0.46         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46         5.19        16.31         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IM TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        2.20         7.82        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC 
        9.67         8.28        10.55       140.81        48.00        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 
       24.66         0.10        12.89         8.94         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP 
       11.93        45.93        22.45         6.12         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE 
       46.78        19.79         1.97        15.19         3.48         3.25 
TCGA-G2-A2EC TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       22.32        30.61         5.69        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OS 
       14.07        17.75         1.12         7.73         2.10        20.98 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        8.75         3.45         4.67 

  ERBB3 MUTATED ERBB3 WILD-TYPE 
           3.12            0.10 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
          61.94          140.81 
  ERBB3 MUTATED ERBB3 WILD-TYPE 
         12.065           8.750 
[1] "3.1 - 61.9 (12.1)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.5"
D20V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ERBB3 MUTATED         0        3         5        5
  ERBB3 WILD-TYPE       1       34        39       39
D20V3, multiclass
           clus
vv          ERBB3 MUTATED ERBB3 WILD-TYPE
  STAGE I               0               1
  STAGE II              3              34
  STAGE III             5              39
  STAGE IV              5              39
[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              T1+T2 T3 T4
  ERBB3 MUTATED       3  6  2
  ERBB3 WILD-TYPE    28 59 15
D20V4, multiclass
       clus
vv      ERBB3 MUTATED ERBB3 WILD-TYPE
  T1+T2             3              28
  T3                6              59
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ERBB3 MUTATED    8  2  3  0
  ERBB3 WILD-TYPE 66 11 21  6
D20V5, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  N0             8              66
  N1             2              11
  N2             3              21
  N3             0               6
[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              M0 M1 MX
  ERBB3 MUTATED    8  0  6
  ERBB3 WILD-TYPE 68  4 43
D20V6, multiclass
    clus
vv   ERBB3 MUTATED ERBB3 WILD-TYPE
  M0             8              68
  M1             0               4
  MX             6              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"
D20V7, binary
                 cls
clus               0  1
  ERBB3 MUTATED    2 12
  ERBB3 WILD-TYPE 30 86
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB3 MUTATED      2   12
  ERBB3 WILD-TYPE   30   86
        clus
vv       ERBB3 MUTATED ERBB3 WILD-TYPE
  FEMALE             2              30
  MALE              12              86
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
D20V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ERBB3 MUTATED       0                         0    13
  ERBB3 WILD-TYPE     8                         6    94
D20V11, multiclass
                           clus
vv                          ERBB3 MUTATED ERBB3 WILD-TYPE
  ASIAN                                 0               8
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                13              94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = FAT1 MUTATION ANALYSIS
D21V1, survival
                sevent
clus2             0  1
  FAT1 MUTATED    9  6
  FAT1 WILD-TYPE 71 39
  FAT1 MUTATED FAT1 WILD-TYPE 
            15            110 
  FAT1 MUTATED FAT1 WILD-TYPE 
             6             39 
$`FAT1 MUTATED`
TCGA-BL-A13I TCGA-BT-A20O TCGA-BT-A20U TCGA-BT-A2LB TCGA-BT-A3PK TCGA-BT-A42B 
        7.33        12.16        14.96         5.59         2.07        15.42 
TCGA-CF-A27C TCGA-CU-A3YL TCGA-DK-A1AG TCGA-DK-A3IQ TCGA-G2-A2EJ TCGA-G2-A2EO 
        0.69        16.31        15.62        10.49        30.61        35.24 
TCGA-GC-A3WC TCGA-GV-A3QI TCGA-K4-A3WS 
       17.75         4.14         8.75 

$`FAT1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         2.66         6.74         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20W 
       32.84        17.88        19.50         5.06        14.89         8.35 
TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
        3.65         4.67        12.82        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO 
       23.01         2.04         0.46         0.43        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20         5.46         5.19         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IS TCGA-DK-A3IT 
        2.20         3.98         7.82         8.22        50.27        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       43.59        24.66         0.10        12.89         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
        6.12        12.82         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC 
        1.97        15.19         3.48         4.08         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       61.94         5.69        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         7.73         2.10         3.12        20.98        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        6.67         6.41        19.07         1.51         6.74        38.60 
TCGA-K4-A3WU TCGA-K4-A3WV 
        3.45         4.67 

  FAT1 MUTATED FAT1 WILD-TYPE 
          0.69           0.10 
  FAT1 MUTATED FAT1 WILD-TYPE 
         35.24         140.81 
  FAT1 MUTATED FAT1 WILD-TYPE 
        12.160          8.315 
[1] "0.7 - 35.2 (12.2)" "0.1 - 140.8 (8.3)"
[1] "hr=" "1.1"
D21V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  FAT1 MUTATED         0        2        11        1
  FAT1 WILD-TYPE       1       35        33       43
D21V3, multiclass
           clus
vv          FAT1 MUTATED FAT1 WILD-TYPE
  STAGE I              0              1
  STAGE II             2             35
  STAGE III           11             33
  STAGE IV             1             43
[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             T1+T2 T3 T4
  FAT1 MUTATED       1 12  1
  FAT1 WILD-TYPE    30 53 16
D21V4, multiclass
       clus
vv      FAT1 MUTATED FAT1 WILD-TYPE
  T1+T2            1             30
  T3              12             53
  T4               1             16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  FAT1 MUTATED   14  1  0  0
  FAT1 WILD-TYPE 60 12 24  6
D21V5, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  N0           14             60
  N1            1             12
  N2            0             24
  N3            0              6
[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             M0 M1 MX
  FAT1 MUTATED    9  0  6
  FAT1 WILD-TYPE 67  4 43
D21V6, multiclass
    clus
vv   FAT1 MUTATED FAT1 WILD-TYPE
  M0            9             67
  M1            0              4
  MX            6             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"
D21V7, binary
                cls
clus              0  1
  FAT1 MUTATED    5 10
  FAT1 WILD-TYPE 27 88
[1] "tbl2"
                cls
clus             [,1] [,2]
  FAT1 MUTATED      5   10
  FAT1 WILD-TYPE   27   88
        clus
vv       FAT1 MUTATED FAT1 WILD-TYPE
  FEMALE            5             27
  MALE             10             88
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
D21V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAT1 MUTATED       1                         0    13
  FAT1 WILD-TYPE     7                         6    94
D21V11, multiclass
                           clus
vv                          FAT1 MUTATED FAT1 WILD-TYPE
  ASIAN                                1              7
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                               13             94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = MLL MUTATION ANALYSIS
D22V1, survival
               sevent
clus2            0  1
  MLL MUTATED   10  8
  MLL WILD-TYPE 70 37
  MLL MUTATED MLL WILD-TYPE 
           18           107 
  MLL MUTATED MLL WILD-TYPE 
            8            37 
$`MLL MUTATED`
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20Q TCGA-BT-A2LB 
        6.74        11.93        19.04        32.84        19.50         5.59 
TCGA-C4-A0F1 TCGA-CF-A1HR TCGA-CU-A0YO TCGA-DK-A1AC TCGA-DK-A2I6 TCGA-DK-A3X1 
        2.93         0.46         4.90       130.88        87.32        48.00 
TCGA-E7-A3Y1 TCGA-FD-A3B6 TCGA-FD-A3N5 TCGA-G2-A3VY TCGA-GC-A3RC TCGA-GC-A3WC 
        0.10         6.87        11.93         0.85        15.91        17.75 

$`MLL WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20O TCGA-BT-A20P 
       40.08         7.33         2.66         6.58        12.16        17.88 
TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH 
        5.06        14.89        14.96         8.35         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         2.07        15.42        28.70         1.94        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YR TCGA-CU-A3KJ 
        2.04         0.43         0.69        12.92         7.20         5.46 
TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.19        16.31         2.53         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
       19.00         8.91       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK TCGA-DK-A3IL 
        1.81        10.59         7.79       123.85         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 
        9.67         8.28        10.55       140.81        43.59        24.66 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ 
       12.89         8.94         4.01        12.43        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       22.45         6.12        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       19.79         1.97        15.19         3.48         4.08         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
       22.32        61.94        30.61         5.69        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
        7.04        20.12         2.89         2.24        15.81         4.50 
TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       14.07         1.12         7.73         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF 
       11.31         4.41         6.41         6.15         5.69         7.63 
TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.79         4.14         6.67         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74        38.60         8.75         3.45         4.67 

  MLL MUTATED MLL WILD-TYPE 
         0.10          0.43 
  MLL MUTATED MLL WILD-TYPE 
       130.88        140.81 
  MLL MUTATED MLL WILD-TYPE 
        11.93          8.75 
[1] "0.1 - 130.9 (11.9)" "0.4 - 140.8 (8.8)" 
[1] "hr=" "1.1"
D22V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  MLL MUTATED         0        6         8        3
  MLL WILD-TYPE       1       31        36       41
D22V3, multiclass
           clus
vv          MLL MUTATED MLL WILD-TYPE
  STAGE I             0             1
  STAGE II            6            31
  STAGE III           8            36
  STAGE IV            3            41
[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            T1+T2 T3 T4
  MLL MUTATED       5 11  0
  MLL WILD-TYPE    26 54 17
D22V4, multiclass
       clus
vv      MLL MUTATED MLL WILD-TYPE
  T1+T2           5            26
  T3             11            54
  T4              0            17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2 N3
  MLL MUTATED   14  1  2  0
  MLL WILD-TYPE 60 12 22  6
D22V5, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  N0          14            60
  N1           1            12
  N2           2            22
  N3           0             6
[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            M0 M1 MX
  MLL MUTATED   11  0  6
  MLL WILD-TYPE 65  4 43
D22V6, multiclass
    clus
vv   MLL MUTATED MLL WILD-TYPE
  M0          11            65
  M1           0             4
  MX           6            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"
D22V7, binary
               cls
clus             0  1
  MLL MUTATED    4 14
  MLL WILD-TYPE 28 84
[1] "tbl2"
               cls
clus            [,1] [,2]
  MLL MUTATED      4   14
  MLL WILD-TYPE   28   84
        clus
vv       MLL MUTATED MLL WILD-TYPE
  FEMALE           4            28
  MALE            14            84
[1] 2 2
[1] FALSE
D22V8, continuous
[1] "Remove cluster labels:" "MLL MUTATED"           
clus
  MLL MUTATED MLL WILD-TYPE 
            2            35 
   TCGA-CF-A1HS    TCGA-CF-A27C    TCGA-CF-A3MF    TCGA-CF-A3MG    TCGA-CF-A3MH 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-CF-A3MI    TCGA-DK-A2HX    TCGA-DK-A3IN    TCGA-DK-A3IV    TCGA-DK-A3WX 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-E5-A2PC    TCGA-G2-A2EC    TCGA-G2-A2EF    TCGA-G2-A2EJ    TCGA-G2-A2EK 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-G2-A2EO    TCGA-G2-A2ES    TCGA-G2-A3IB    TCGA-G2-A3IE    TCGA-GC-A3BM 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-GC-A3I6    TCGA-GC-A3OO    TCGA-GC-A3RD    TCGA-GC-A3YS    TCGA-GD-A3OS 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-GV-A3JV    TCGA-GV-A3JW    TCGA-GV-A3JX    TCGA-GV-A3JZ    TCGA-GV-A3QF 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
   TCGA-GV-A3QH    TCGA-GV-A3QI    TCGA-GV-A3QK    TCGA-GV-A40E    TCGA-GV-A40G 
"MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" "MLL WILD-TYPE" 
D22V9, continuous
D22V10, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MLL MUTATED       2                         1    13
  MLL WILD-TYPE     6                         5    94
D22V11, multiclass
                           clus
vv                          MLL MUTATED MLL WILD-TYPE
  ASIAN                               2             6
  BLACK OR AFRICAN AMERICAN           1             5
  WHITE                              13            94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = HRAS MUTATION ANALYSIS
D23V1, survival
                sevent
clus2             0  1
  HRAS MUTATED    3  2
  HRAS WILD-TYPE 77 43
  HRAS MUTATED HRAS WILD-TYPE 
             5            120 
  HRAS MUTATED HRAS WILD-TYPE 
             2             43 
$`HRAS MUTATED`
TCGA-BT-A2LB TCGA-DK-A1AC TCGA-FT-A3EE TCGA-G2-A2EJ TCGA-GD-A3OQ 
        5.59       130.88         3.25        30.61         3.12 

$`HRAS WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89        14.96         8.35         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.04         0.46         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46         5.19        16.31         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE 
       66.41        18.41        19.00         8.91       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
      140.81        48.00        43.59        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       46.78        19.79         1.97        15.19         3.48         4.08 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       22.32        61.94         5.69        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98        11.31         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  HRAS MUTATED HRAS WILD-TYPE 
          3.12           0.10 
  HRAS MUTATED HRAS WILD-TYPE 
        130.88         140.81 
  HRAS MUTATED HRAS WILD-TYPE 
         5.590          8.925 
[1] "3.1 - 130.9 (5.6)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  HRAS MUTATED         0        2         3        1
  HRAS WILD-TYPE       1       35        41       43
D23V3, multiclass
           clus
vv          HRAS MUTATED HRAS WILD-TYPE
  STAGE I              0              1
  STAGE II             2             35
  STAGE III            3             41
  STAGE IV             1             43
[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             T1+T2 T3 T4
  HRAS MUTATED       1  2  2
  HRAS WILD-TYPE    30 63 15
D23V4, multiclass
       clus
vv      HRAS MUTATED HRAS WILD-TYPE
  T1+T2            1             30
  T3               2             63
  T4               2             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  HRAS MUTATED    5  1  0  0
  HRAS WILD-TYPE 69 12 24  6
D23V5, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  N0            5             69
  N1            1             12
  N2            0             24
  N3            0              6
[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             M0 M1 MX
  HRAS MUTATED    4  0  2
  HRAS WILD-TYPE 72  4 47
D23V6, multiclass
    clus
vv   HRAS MUTATED HRAS WILD-TYPE
  M0            4             72
  M1            0              4
  MX            2             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                cls
clus              0  1
  HRAS MUTATED    3  3
  HRAS WILD-TYPE 29 95
[1] "tbl2"
                cls
clus             [,1] [,2]
  HRAS MUTATED      3    3
  HRAS WILD-TYPE   29   95
        clus
vv       HRAS MUTATED HRAS WILD-TYPE
  FEMALE            3             29
  MALE              3             95
[1] 2 2
[1] FALSE
D23V8, continuous
[1] "Remove cluster labels:" "HRAS MUTATED"          
clus
  HRAS MUTATED HRAS WILD-TYPE 
             2             35 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-DK-A2HX     TCGA-DK-A3IN     TCGA-DK-A3IV 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-E5-A2PC     TCGA-G2-A2EC     TCGA-G2-A2EF 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G2-A2EK     TCGA-G2-A2EO     TCGA-G2-A2ES     TCGA-G2-A3IB 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-G2-A3IE     TCGA-G2-A3VY     TCGA-GC-A3BM     TCGA-GC-A3I6 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-GC-A3OO     TCGA-GC-A3RC     TCGA-GC-A3RD     TCGA-GC-A3YS 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GV-A3JV     TCGA-GV-A3JW     TCGA-GV-A3JX 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QH     TCGA-GV-A3QI 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G 
"HRAS WILD-TYPE" "HRAS WILD-TYPE" "HRAS WILD-TYPE" 
D23V9, continuous
D23V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  HRAS MUTATED       1                         0     5
  HRAS WILD-TYPE     7                         6   102
D23V11, multiclass
                           clus
vv                          HRAS MUTATED HRAS WILD-TYPE
  ASIAN                                1              7
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                5            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = ACRC MUTATION ANALYSIS
D24V1, survival
                sevent
clus2             0  1
  ACRC MUTATED    2  1
  ACRC WILD-TYPE 78 44
  ACRC MUTATED ACRC WILD-TYPE 
             3            122 
  ACRC MUTATED ACRC WILD-TYPE 
             1             44 
$`ACRC MUTATED`
TCGA-FD-A3SJ TCGA-GC-A3I6 TCGA-GV-A3QI 
       24.30         2.24         4.14 

$`ACRC WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
       12.82         2.07        15.42        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN 
       23.01         2.04         0.46         0.43         0.69        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        4.90         7.20         5.46         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 
        8.28        10.55       140.81        48.00        43.59        24.66 
TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.10        12.89         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       11.93        45.93        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
       13.18        46.78        19.79         1.97        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS 
       15.81         4.50        15.91        14.07        17.75         1.12 
TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV 
        7.73         2.10         3.12        20.98        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QK 
        6.41         6.15         5.69         7.63         7.79         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV 
        3.45         4.67 

  ACRC MUTATED ACRC WILD-TYPE 
          2.24           0.10 
  ACRC MUTATED ACRC WILD-TYPE 
         24.30         140.81 
  ACRC MUTATED ACRC WILD-TYPE 
         4.140          8.925 
[1] "2.2 - 24.3 (4.1)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.1"
D24V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ACRC MUTATED         0        0         3        1
  ACRC WILD-TYPE       1       37        41       43
D24V3, multiclass
           clus
vv          ACRC MUTATED ACRC WILD-TYPE
  STAGE I              0              1
  STAGE II             0             37
  STAGE III            3             41
  STAGE IV             1             43
[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             T1+T2 T3 T4
  ACRC MUTATED       1  3  0
  ACRC WILD-TYPE    30 62 17
D24V4, multiclass
       clus
vv      ACRC MUTATED ACRC WILD-TYPE
  T1+T2            1             30
  T3               3             62
  T4               0             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ACRC MUTATED    3  0  1  0
  ACRC WILD-TYPE 71 13 23  6
D24V5, multiclass
    clus
vv   ACRC MUTATED ACRC WILD-TYPE
  N0            3             71
  N1            0             13
  N2            1             23
  N3            0              6
[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             M0 M1 MX
  ACRC MUTATED    2  0  2
  ACRC WILD-TYPE 74  4 47
D24V6, multiclass
    clus
vv   ACRC MUTATED ACRC WILD-TYPE
  M0            2             74
  M1            0              4
  MX            2             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                cls
clus              0  1
  ACRC MUTATED    0  4
  ACRC WILD-TYPE 32 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  ACRC MUTATED      0    4
  ACRC WILD-TYPE   32   94
        clus
vv       ACRC MUTATED ACRC WILD-TYPE
  FEMALE            0             32
  MALE              4             94
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
[1] "Remove cluster labels:" "ACRC MUTATED"          
clus
  ACRC MUTATED ACRC WILD-TYPE 
             2             75 
    TCGA-BL-A0C8     TCGA-BL-A13I     TCGA-BL-A13J     TCGA-BL-A3JM 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-BT-A20J     TCGA-BT-A20N     TCGA-BT-A42B     TCGA-BT-A42C 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-C4-A0F0     TCGA-C4-A0F1     TCGA-C4-A0F6     TCGA-CF-A3MH 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-CF-A3MI     TCGA-CU-A0YN     TCGA-CU-A0YR     TCGA-CU-A3KJ 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-CU-A3QU     TCGA-CU-A3YL     TCGA-DK-A1A3     TCGA-DK-A1A5 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-DK-A1A6     TCGA-DK-A1AA     TCGA-DK-A1AC     TCGA-DK-A1AE 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-DK-A2HX     TCGA-DK-A2I6     TCGA-DK-A3IL     TCGA-DK-A3IM 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-DK-A3IN     TCGA-DK-A3IQ     TCGA-DK-A3IU     TCGA-DK-A3IV 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-DK-A3WX     TCGA-DK-A3X1     TCGA-FD-A3B3     TCGA-FD-A3B5 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-FD-A3B6     TCGA-FD-A3B7     TCGA-FD-A3B8     TCGA-FD-A3N5 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-FD-A3NA     TCGA-FD-A3SM     TCGA-FD-A3SN     TCGA-FD-A3SO 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-FD-A3SP     TCGA-FD-A3SQ     TCGA-FD-A3SR     TCGA-FD-A3SS 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-FJ-A3ZE     TCGA-FJ-A3ZF     TCGA-G2-A2EF     TCGA-G2-A2EJ 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-G2-A2ES     TCGA-G2-A3IE     TCGA-GC-A3BM     TCGA-GC-A3RB 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-GC-A3WC     TCGA-GC-A3YS     TCGA-GD-A2C5     TCGA-GD-A3OQ 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-GD-A3OS     TCGA-GU-A42R     TCGA-GV-A3JV     TCGA-GV-A3JX 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-GV-A3JZ     TCGA-GV-A3QF     TCGA-GV-A3QG     TCGA-GV-A3QH 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G     TCGA-H4-A2HO 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
    TCGA-H4-A2HQ     TCGA-K4-A3WS     TCGA-K4-A3WV 
"ACRC WILD-TYPE" "ACRC WILD-TYPE" "ACRC WILD-TYPE" 
D24V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ACRC MUTATED       1                         0     3
  ACRC WILD-TYPE     7                         6   104
D24V11, multiclass
                           clus
vv                          ACRC MUTATED ACRC WILD-TYPE
  ASIAN                                1              7
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                3            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = TXNIP MUTATION ANALYSIS
D25V1, survival
                 sevent
clus2              0  1
  TXNIP MUTATED    5  4
  TXNIP WILD-TYPE 75 41
  TXNIP MUTATED TXNIP WILD-TYPE 
              9             116 
  TXNIP MUTATED TXNIP WILD-TYPE 
              4              41 
$`TXNIP MUTATED`
TCGA-BT-A20T TCGA-BT-A3PH TCGA-DK-A1A6 TCGA-FD-A3SO TCGA-G2-A2EC TCGA-G2-A2EO 
       14.89         4.67        66.41         5.52        22.32        35.24 
TCGA-GC-A3WC TCGA-GV-A40G TCGA-K4-A3WU 
       17.75        19.07         3.45 

$`TXNIP WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.96         8.35         5.59         3.65        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       15.42        28.70         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.46         0.43         0.69        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A7 
        5.46         5.19        16.31         2.53         2.14        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       15.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS 
        2.20         3.98         7.82         8.22        10.49        50.27 
TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY 
       21.30        20.02         9.67         8.28        10.55       140.81 
TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
       48.00        43.59        24.66         0.10        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45         6.12        12.82        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EF 
        1.97        15.19         3.48         4.08         3.25        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY 
       30.61         5.69        17.26         7.04        20.12         0.85 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         7.73         2.10         3.12        20.98        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE 
        4.14         6.67         6.41         1.51         6.74        38.60 
TCGA-K4-A3WS TCGA-K4-A3WV 
        8.75         4.67 

  TXNIP MUTATED TXNIP WILD-TYPE 
           3.45            0.10 
  TXNIP MUTATED TXNIP WILD-TYPE 
          66.41          140.81 
  TXNIP MUTATED TXNIP WILD-TYPE 
          17.75            8.55 
[1] "3.5 - 66.4 (17.8)" "0.1 - 140.8 (8.6)"
[1] "hr=" "1.1"
D25V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  TXNIP MUTATED         0        2         3        4
  TXNIP WILD-TYPE       1       35        41       40
D25V3, multiclass
           clus
vv          TXNIP MUTATED TXNIP WILD-TYPE
  STAGE I               0               1
  STAGE II              2              35
  STAGE III             3              41
  STAGE IV              4              40
[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              T1+T2 T3 T4
  TXNIP MUTATED       2  5  1
  TXNIP WILD-TYPE    29 60 16
D25V4, multiclass
       clus
vv      TXNIP MUTATED TXNIP WILD-TYPE
  T1+T2             2              29
  T3                5              60
  T4                1              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  TXNIP MUTATED    5  3  1  0
  TXNIP WILD-TYPE 69 10 23  6
D25V5, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  N0             5              69
  N1             3              10
  N2             1              23
  N3             0               6
[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              M0 M1 MX
  TXNIP MUTATED    4  0  5
  TXNIP WILD-TYPE 72  4 44
D25V6, multiclass
    clus
vv   TXNIP MUTATED TXNIP WILD-TYPE
  M0             4              72
  M1             0               4
  MX             5              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"
D25V7, binary
                 cls
clus               0  1
  TXNIP MUTATED    2  7
  TXNIP WILD-TYPE 30 91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TXNIP MUTATED      2    7
  TXNIP WILD-TYPE   30   91
        clus
vv       TXNIP MUTATED TXNIP WILD-TYPE
  FEMALE             2              30
  MALE               7              91
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
D25V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TXNIP MUTATED       0                         1     7
  TXNIP WILD-TYPE     8                         5   100
D25V11, multiclass
                           clus
vv                          TXNIP MUTATED TXNIP WILD-TYPE
  ASIAN                                 0               8
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 7             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = ECM1 MUTATION ANALYSIS
D26V1, survival
                sevent
clus2             0  1
  ECM1 MUTATED    3  2
  ECM1 WILD-TYPE 77 43
  ECM1 MUTATED ECM1 WILD-TYPE 
             5            120 
  ECM1 MUTATED ECM1 WILD-TYPE 
             2             43 
$`ECM1 MUTATED`
TCGA-DK-A2I4 TCGA-DK-A3IU TCGA-FD-A3SO TCGA-GD-A2C5 TCGA-GV-A3QH 
      123.85        20.02         5.52         7.73         7.79 

$`ECM1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
       12.82         2.07        15.42        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN 
       23.01         2.04         0.46         0.43         0.69        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        4.90         7.20         5.46         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
        7.79        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       10.49        50.27        21.30         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
      140.81        48.00        43.59        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45         6.12        12.82        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE 
       19.79         1.97        15.19         3.48         4.08         3.25 
TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES 
       22.32        61.94        30.61         5.69        35.24        17.26 
TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO 
        7.04        20.12         0.85         2.89         2.24        15.81 
TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A3OP 
        4.50        15.91        14.07        17.75         1.12         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12        20.98        11.31         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        5.69         7.63         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  ECM1 MUTATED ECM1 WILD-TYPE 
          5.52           0.10 
  ECM1 MUTATED ECM1 WILD-TYPE 
        123.85         140.81 
  ECM1 MUTATED ECM1 WILD-TYPE 
         7.790          8.925 
[1] "5.5 - 123.8 (7.8)" "0.1 - 140.8 (8.9)"
[1] "hr=" "1.1"
D26V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  ECM1 MUTATED         0        2         1        2
  ECM1 WILD-TYPE       1       35        43       42
D26V3, multiclass
           clus
vv          ECM1 MUTATED ECM1 WILD-TYPE
  STAGE I              0              1
  STAGE II             2             35
  STAGE III            1             43
  STAGE IV             2             42
[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             T1+T2 T3 T4
  ECM1 MUTATED       1  3  0
  ECM1 WILD-TYPE    30 62 17
D26V4, multiclass
       clus
vv      ECM1 MUTATED ECM1 WILD-TYPE
  T1+T2            1             30
  T3               3             62
  T4               0             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  ECM1 MUTATED    2  1  1  0
  ECM1 WILD-TYPE 72 12 23  6
D26V5, multiclass
    clus
vv   ECM1 MUTATED ECM1 WILD-TYPE
  N0            2             72
  N1            1             12
  N2            1             23
  N3            0              6
[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             M0 M1 MX
  ECM1 MUTATED    2  0  3
  ECM1 WILD-TYPE 74  4 46
D26V6, multiclass
    clus
vv   ECM1 MUTATED ECM1 WILD-TYPE
  M0            2             74
  M1            0              4
  MX            3             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"
D26V7, binary
                cls
clus              0  1
  ECM1 MUTATED    1  4
  ECM1 WILD-TYPE 31 94
[1] "tbl2"
                cls
clus             [,1] [,2]
  ECM1 MUTATED      1    4
  ECM1 WILD-TYPE   31   94
        clus
vv       ECM1 MUTATED ECM1 WILD-TYPE
  FEMALE            1             31
  MALE              4             94
[1] 2 2
[1] FALSE
D26V8, continuous
[1] "Remove cluster labels:" "ECM1 MUTATED"          
clus
  ECM1 MUTATED ECM1 WILD-TYPE 
             1             36 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-DK-A2HX     TCGA-DK-A3IN 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-DK-A3IV     TCGA-DK-A3WX     TCGA-E5-A2PC     TCGA-G2-A2EC 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-G2-A2EF     TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EO 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-G2-A2ES     TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A3YS     TCGA-GD-A3OS     TCGA-GV-A3JV 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-GV-A3JW     TCGA-GV-A3JX     TCGA-GV-A3JZ     TCGA-GV-A3QF 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
    TCGA-GV-A3QI     TCGA-GV-A3QK     TCGA-GV-A40E     TCGA-GV-A40G 
"ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" "ECM1 WILD-TYPE" 
D26V9, continuous
D26V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ECM1 MUTATED       0                         0     5
  ECM1 WILD-TYPE     8                         6   102
D26V11, multiclass
                           clus
vv                          ECM1 MUTATED ECM1 WILD-TYPE
  ASIAN                                0              8
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                5            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = KLF5 MUTATION ANALYSIS
D27V1, survival
                sevent
clus2             0  1
  KLF5 MUTATED    7  3
  KLF5 WILD-TYPE 73 42
  KLF5 MUTATED KLF5 WILD-TYPE 
            10            115 
  KLF5 MUTATED KLF5 WILD-TYPE 
             3             42 
$`KLF5 MUTATED`
TCGA-BL-A3JM TCGA-BT-A0YX TCGA-BT-A42C TCGA-C4-A0F6 TCGA-DK-A3IU TCGA-DK-A3X1 
        6.74        11.93        28.70        23.01        20.02        48.00 
TCGA-E7-A3Y1 TCGA-FD-A3SS TCGA-GC-A3WC TCGA-GV-A3QK 
        0.10         1.97        17.75         6.67 

$`KLF5 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A20J TCGA-BT-A20N 
       40.08         7.33         2.66         6.58        19.04        32.84 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20T TCGA-BT-A20U 
       12.16        17.88        19.50         5.06        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
        8.35         5.59         3.65         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS 
       15.42         1.94         2.93         2.04         0.46         0.43 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.69        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK 
        1.81        10.59         7.79       123.85        87.32         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 
        9.67         8.28        10.55       140.81        43.59        24.66 
TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 
       12.89         8.94         6.87         4.01        12.43        11.93 
TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO 
       45.93        24.30        22.45         6.12        12.82         5.52 
TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       13.18        46.78        19.79        15.19         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25        22.32        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3YS TCGA-GD-A2C5 
       15.81         4.50        15.91        14.07         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E 
        6.15         5.69         7.63         7.79         4.14         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  KLF5 MUTATED KLF5 WILD-TYPE 
          0.10           0.43 
  KLF5 MUTATED KLF5 WILD-TYPE 
         48.00         140.81 
  KLF5 MUTATED KLF5 WILD-TYPE 
         14.84           8.75 
[1] "0.1 - 48.0 (14.8)" "0.4 - 140.8 (8.8)"
[1] "hr=" "1.5"
D27V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  KLF5 MUTATED         0        3         5        2
  KLF5 WILD-TYPE       1       34        39       42
D27V3, multiclass
           clus
vv          KLF5 MUTATED KLF5 WILD-TYPE
  STAGE I              0              1
  STAGE II             3             34
  STAGE III            5             39
  STAGE IV             2             42
[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             T1+T2 T3 T4
  KLF5 MUTATED       1  5  2
  KLF5 WILD-TYPE    30 60 15
D27V4, multiclass
       clus
vv      KLF5 MUTATED KLF5 WILD-TYPE
  T1+T2            1             30
  T3               5             60
  T4               2             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2 N3
  KLF5 MUTATED    8  0  1  1
  KLF5 WILD-TYPE 66 13 23  5
D27V5, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  N0            8             66
  N1            0             13
  N2            1             23
  N3            1              5
[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             M0 M1 MX
  KLF5 MUTATED    8  0  2
  KLF5 WILD-TYPE 68  4 47
D27V6, multiclass
    clus
vv   KLF5 MUTATED KLF5 WILD-TYPE
  M0            8             68
  M1            0              4
  MX            2             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                cls
clus              0  1
  KLF5 MUTATED    5  5
  KLF5 WILD-TYPE 27 93
[1] "tbl2"
                cls
clus             [,1] [,2]
  KLF5 MUTATED      5    5
  KLF5 WILD-TYPE   27   93
        clus
vv       KLF5 MUTATED KLF5 WILD-TYPE
  FEMALE            5             27
  MALE              5             93
[1] 2 2
[1] FALSE
D27V8, continuous
[1] "Remove cluster labels:" "KLF5 MUTATED"          
clus
  KLF5 MUTATED KLF5 WILD-TYPE 
             1             36 
    TCGA-CF-A1HS     TCGA-CF-A27C     TCGA-CF-A3MF     TCGA-CF-A3MG 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-CF-A3MH     TCGA-CF-A3MI     TCGA-DK-A2HX     TCGA-DK-A3IN 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-DK-A3IV     TCGA-DK-A3WX     TCGA-E5-A2PC     TCGA-G2-A2EC 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-G2-A2EF     TCGA-G2-A2EJ     TCGA-G2-A2EK     TCGA-G2-A2EO 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-G2-A2ES     TCGA-G2-A3IB     TCGA-G2-A3IE     TCGA-G2-A3VY 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-GC-A3BM     TCGA-GC-A3I6     TCGA-GC-A3OO     TCGA-GC-A3RC 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-GC-A3RD     TCGA-GC-A3YS     TCGA-GD-A3OS     TCGA-GV-A3JV 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-GV-A3JW     TCGA-GV-A3JX     TCGA-GV-A3JZ     TCGA-GV-A3QF 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
    TCGA-GV-A3QH     TCGA-GV-A3QI     TCGA-GV-A40E     TCGA-GV-A40G 
"KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" "KLF5 WILD-TYPE" 
D27V9, continuous
D27V10, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KLF5 MUTATED       0                         0     9
  KLF5 WILD-TYPE     8                         6    98
D27V11, multiclass
                           clus
vv                          KLF5 MUTATED KLF5 WILD-TYPE
  ASIAN                                0              8
  BLACK OR AFRICAN AMERICAN            0              6
  WHITE                                9             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = RBM26 MUTATION ANALYSIS
D28V1, survival
                 sevent
clus2              0  1
  RBM26 MUTATED    6  3
  RBM26 WILD-TYPE 74 42
  RBM26 MUTATED RBM26 WILD-TYPE 
              9             116 
  RBM26 MUTATED RBM26 WILD-TYPE 
              3              42 
$`RBM26 MUTATED`
TCGA-BL-A3JM TCGA-BT-A20R TCGA-BT-A3PJ TCGA-CF-A27C TCGA-DK-A2HX TCGA-DK-A2I4 
        6.74         5.06        12.82         0.69         1.81       123.85 
TCGA-E7-A3X6 TCGA-FD-A3B5 TCGA-GC-A3RD 
       24.66         8.94        14.07 

$`RBM26 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BT-A0S7 TCGA-BT-A0YX TCGA-BT-A20J 
       40.08         7.33         2.66         6.58        11.93        19.04 
TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20T TCGA-BT-A20U 
       32.84        12.16        17.88        19.50        14.89        14.96 
TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PK TCGA-BT-A42B 
        8.35         5.59         3.65         4.67         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR 
       28.70         1.94         2.93        23.01         2.04         0.46 
TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.43        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG 
        8.91       130.88       112.44        16.14        17.62        15.62 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
       10.59         7.79        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3Y1 
        8.28        10.55       140.81        48.00        43.59         0.10 
TCGA-FD-A3B3 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
       12.89         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP 
       24.30        22.45         6.12        12.82         5.52        13.18 
TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF 
       46.78        19.79         1.97        15.19         3.48         4.08 
TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO 
        3.25        22.32        61.94        30.61         5.69        35.24 
TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 
       17.26         7.04        20.12         0.85         2.89         2.24 
TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 
       15.81         4.50        15.91        17.75         1.12         7.73 
TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW 
        2.10         3.12        20.98        11.31         4.41         6.41 
TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.15         5.69         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV 
        3.45         4.67 

  RBM26 MUTATED RBM26 WILD-TYPE 
           0.69            0.10 
  RBM26 MUTATED RBM26 WILD-TYPE 
         123.85          140.81 
  RBM26 MUTATED RBM26 WILD-TYPE 
           8.94            8.83 
[1] "0.7 - 123.8 (8.9)" "0.1 - 140.8 (8.8)"
[1] "hr=" "1.1"
D28V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  RBM26 MUTATED         0        1         4        3
  RBM26 WILD-TYPE       1       36        40       41
D28V3, multiclass
           clus
vv          RBM26 MUTATED RBM26 WILD-TYPE
  STAGE I               0               1
  STAGE II              1              36
  STAGE III             4              40
  STAGE IV              3              41
[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              T1+T2 T3 T4
  RBM26 MUTATED       2  7  0
  RBM26 WILD-TYPE    29 58 17
D28V4, multiclass
       clus
vv      RBM26 MUTATED RBM26 WILD-TYPE
  T1+T2             2              29
  T3                7              58
  T4                0              17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  RBM26 MUTATED    4  2  1  1
  RBM26 WILD-TYPE 70 11 23  5
D28V5, multiclass
    clus
vv   RBM26 MUTATED RBM26 WILD-TYPE
  N0             4              70
  N1             2              11
  N2             1              23
  N3             1               5
[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              M0 M1 MX
  RBM26 MUTATED    8  0  1
  RBM26 WILD-TYPE 68  4 48
D28V6, multiclass
    clus
vv   RBM26 MUTATED RBM26 WILD-TYPE
  M0             8              68
  M1             0               4
  MX             1              48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                 cls
clus               0  1
  RBM26 MUTATED    3  6
  RBM26 WILD-TYPE 29 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM26 MUTATED      3    6
  RBM26 WILD-TYPE   29   92
        clus
vv       RBM26 MUTATED RBM26 WILD-TYPE
  FEMALE             3              29
  MALE               6              92
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
D28V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBM26 MUTATED       1                         1     7
  RBM26 WILD-TYPE     7                         5   100
D28V11, multiclass
                           clus
vv                          RBM26 MUTATED RBM26 WILD-TYPE
  ASIAN                                 1               7
  BLACK OR AFRICAN AMERICAN             1               5
  WHITE                                 7             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = RAD51C MUTATION ANALYSIS
D29V1, survival
                  sevent
clus2               0  1
  RAD51C MUTATED    2  2
  RAD51C WILD-TYPE 78 43
  RAD51C MUTATED RAD51C WILD-TYPE 
               4              121 
  RAD51C MUTATED RAD51C WILD-TYPE 
               2               43 
$`RAD51C MUTATED`
TCGA-BT-A2LB TCGA-DK-A1A3 TCGA-FD-A3N5 TCGA-FD-A3SN 
        5.59         2.53        11.93        12.82 

$`RAD51C WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89        14.96         8.35         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.04         0.46         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1A6 
        7.20         5.46         5.19        16.31         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
      140.81        48.00        43.59        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3NA TCGA-FD-A3SJ 
        8.94         6.87         4.01        12.43        45.93        24.30 
TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       22.45         6.12         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC 
        1.97        15.19         3.48         4.08         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12        20.98        11.31         4.41         6.41         6.15 
TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E 
        5.69         7.63         7.79         4.14         6.67         6.41 
TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU 
       19.07         1.51         6.74        38.60         8.75         3.45 
TCGA-K4-A3WV 
        4.67 

  RAD51C MUTATED RAD51C WILD-TYPE 
            2.53             0.10 
  RAD51C MUTATED RAD51C WILD-TYPE 
           12.82           140.81 
  RAD51C MUTATED RAD51C WILD-TYPE 
            8.76             8.91 
[1] "2.5 - 12.8 (8.8)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "2.1"
D29V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  RAD51C MUTATED         0        1         1        2
  RAD51C WILD-TYPE       1       36        43       42
D29V3, multiclass
           clus
vv          RAD51C MUTATED RAD51C WILD-TYPE
  STAGE I                0                1
  STAGE II               1               36
  STAGE III              1               43
  STAGE IV               2               42
[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               T1+T2 T3 T4
  RAD51C MUTATED       1  3  0
  RAD51C WILD-TYPE    30 62 17
D29V4, multiclass
       clus
vv      RAD51C MUTATED RAD51C WILD-TYPE
  T1+T2              1               30
  T3                 3               62
  T4                 0               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  RAD51C MUTATED    3  0  1  0
  RAD51C WILD-TYPE 71 13 23  6
D29V5, multiclass
    clus
vv   RAD51C MUTATED RAD51C WILD-TYPE
  N0              3               71
  N1              0               13
  N2              1               23
  N3              0                6
[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               M0 M1 MX
  RAD51C MUTATED    2  0  2
  RAD51C WILD-TYPE 74  4 47
D29V6, multiclass
    clus
vv   RAD51C MUTATED RAD51C WILD-TYPE
  M0              2               74
  M1              0                4
  MX              2               47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                  cls
clus                0  1
  RAD51C MUTATED    1  3
  RAD51C WILD-TYPE 31 95
[1] "tbl2"
                  cls
clus               [,1] [,2]
  RAD51C MUTATED      1    3
  RAD51C WILD-TYPE   31   95
        clus
vv       RAD51C MUTATED RAD51C WILD-TYPE
  FEMALE              1               31
  MALE                3               95
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
D29V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RAD51C MUTATED       0                         1     3
  RAD51C WILD-TYPE     8                         5   104
D29V11, multiclass
                           clus
vv                          RAD51C MUTATED RAD51C WILD-TYPE
  ASIAN                                  0                8
  BLACK OR AFRICAN AMERICAN              1                5
  WHITE                                  3              104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = CEP192 MUTATION ANALYSIS
D30V1, survival
                  sevent
clus2               0  1
  CEP192 MUTATED    4  1
  CEP192 WILD-TYPE 76 44
  CEP192 MUTATED CEP192 WILD-TYPE 
               5              120 
  CEP192 MUTATED CEP192 WILD-TYPE 
               1               44 
$`CEP192 MUTATED`
TCGA-DK-A3WW TCGA-DK-A3X1 TCGA-FD-A3SM TCGA-FD-A3SN TCGA-GV-A3JZ 
        8.28        48.00         6.12        12.82         5.69 

$`CEP192 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 
       12.82         2.07        15.42        28.70         1.94         2.93 
TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN 
       23.01         2.04         0.46         0.43         0.69        12.92 
TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 
        4.90         7.20         5.46         5.19        16.31         2.53 
TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC 
        2.14        66.41        18.41        19.00         8.91       130.88 
TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 
      112.44        16.14        17.62        15.62         1.81        10.59 
TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM 
        7.79       123.85        87.32         2.20         3.98         7.82 
TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV 
        8.22        10.49        50.27        21.30        20.02         9.67 
TCGA-DK-A3WX TCGA-DK-A3WY TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
       10.55       140.81        43.59        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR 
       24.30        22.45         5.52        13.18        46.78        19.79 
TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC 
        1.97        15.19         3.48         4.08         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        35.24        17.26         7.04 
TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB 
       20.12         0.85         2.89         2.24        15.81         4.50 
TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP 
       15.91        14.07        17.75         1.12         7.73         2.10 
TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX 
        3.12        20.98        11.31         4.41         6.41         6.15 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  CEP192 MUTATED CEP192 WILD-TYPE 
            5.69             0.10 
  CEP192 MUTATED CEP192 WILD-TYPE 
           48.00           140.81 
  CEP192 MUTATED CEP192 WILD-TYPE 
           8.280            8.925 
[1] "5.7 - 48.0 (8.3)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "2"  
D30V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  CEP192 MUTATED         0        0         2        3
  CEP192 WILD-TYPE       1       37        42       41
D30V3, multiclass
           clus
vv          CEP192 MUTATED CEP192 WILD-TYPE
  STAGE I                0                1
  STAGE II               0               37
  STAGE III              2               42
  STAGE IV               3               41
[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               T1+T2 T3 T4
  CEP192 MUTATED       0  4  1
  CEP192 WILD-TYPE    31 61 16
D30V4, multiclass
       clus
vv      CEP192 MUTATED CEP192 WILD-TYPE
  T1+T2              0               31
  T3                 4               61
  T4                 1               16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  CEP192 MUTATED    3  0  1  1
  CEP192 WILD-TYPE 71 13 23  5
D30V5, multiclass
    clus
vv   CEP192 MUTATED CEP192 WILD-TYPE
  N0              3               71
  N1              0               13
  N2              1               23
  N3              1                5
[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               M0 M1 MX
  CEP192 MUTATED    2  1  2
  CEP192 WILD-TYPE 74  3 47
D30V6, multiclass
    clus
vv   CEP192 MUTATED CEP192 WILD-TYPE
  M0              2               74
  M1              1                3
  MX              2               47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                  cls
clus                0  1
  CEP192 MUTATED    1  4
  CEP192 WILD-TYPE 31 94
[1] "tbl2"
                  cls
clus               [,1] [,2]
  CEP192 MUTATED      1    4
  CEP192 WILD-TYPE   31   94
        clus
vv       CEP192 MUTATED CEP192 WILD-TYPE
  FEMALE              1               31
  MALE                4               94
[1] 2 2
[1] FALSE
D30V8, continuous
[1] "Remove cluster labels:" "CEP192 MUTATED"        
clus
  CEP192 MUTATED CEP192 WILD-TYPE 
               1               36 
      TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-DK-A2HX       TCGA-DK-A3IN 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-DK-A3IV       TCGA-DK-A3WX       TCGA-E5-A2PC       TCGA-G2-A2EC 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-G2-A2EF       TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EO 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-G2-A3VY 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-GC-A3BM       TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3YS       TCGA-GD-A3OS       TCGA-GV-A3JV 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-GV-A3JW       TCGA-GV-A3JX       TCGA-GV-A3QF       TCGA-GV-A3QH 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" "CEP192 WILD-TYPE" 
D30V9, continuous
D30V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CEP192 MUTATED       0                         0     5
  CEP192 WILD-TYPE     8                         6   102
D30V11, multiclass
                           clus
vv                          CEP192 MUTATED CEP192 WILD-TYPE
  ASIAN                                  0                8
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  5              102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = ASXL2 MUTATION ANALYSIS
D31V1, survival
                 sevent
clus2              0  1
  ASXL2 MUTATED    5  4
  ASXL2 WILD-TYPE 75 41
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              9             116 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              4              41 
$`ASXL2 MUTATED`
TCGA-BT-A0YX TCGA-BT-A20N TCGA-BT-A20T TCGA-CF-A1HR TCGA-DK-A1AC TCGA-E7-A3X6 
       11.93        32.84        14.89         0.46       130.88        24.66 
TCGA-FD-A3SS TCGA-GD-A2C5 TCGA-GV-A3JZ 
        1.97         7.73         5.69 

$`ASXL2 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A20J 
       40.08         7.33         2.66         6.74         6.58        19.04 
TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R TCGA-BT-A20U TCGA-BT-A20W 
       12.16        17.88        19.50         5.06        14.96         8.35 
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B 
        5.59         3.65         4.67        12.82         2.07        15.42 
TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 TCGA-CF-A1HS 
       28.70         1.94         2.93        23.01         2.04         0.43 
TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU 
        0.69        12.92         4.90         7.20         5.46         5.19 
TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA 
       16.31         2.53         2.14        66.41        18.41        19.00 
TCGA-DK-A1AB TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX 
        8.91       112.44        16.14        17.62        15.62         1.81 
TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL 
       10.59         7.79       123.85        87.32         2.20         3.98 
TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU 
        7.82         8.22        10.49        50.27        21.30        20.02 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC 
        9.67         8.28        10.55       140.81        48.00        43.59 
TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 
        0.10        12.89         8.94         6.87         4.01        12.43 
TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM TCGA-FD-A3SN 
       11.93        45.93        24.30        22.45         6.12        12.82 
TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FJ-A3Z7 TCGA-FJ-A3ZE 
        5.52        13.18        46.78        19.79        15.19         3.48 
TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK 
        4.08         3.25        22.32        61.94        30.61         5.69 
TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-G2-A3VY TCGA-GC-A3BM 
       35.24        17.26         7.04        20.12         0.85         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV 
        1.12         2.10         3.12        20.98        11.31         4.41 
TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK 
        6.41         6.15         7.63         7.79         4.14         6.67 
TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS 
        6.41        19.07         1.51         6.74        38.60         8.75 
TCGA-K4-A3WU TCGA-K4-A3WV 
        3.45         4.67 

  ASXL2 MUTATED ASXL2 WILD-TYPE 
           0.46            0.10 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
         130.88          140.81 
  ASXL2 MUTATED ASXL2 WILD-TYPE 
          11.93            8.83 
[1] "0.5 - 130.9 (11.9)" "0.1 - 140.8 (8.8)" 
[1] "hr=" "1.1"
D31V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ASXL2 MUTATED         0        1         3        4
  ASXL2 WILD-TYPE       1       36        41       40
D31V3, multiclass
           clus
vv          ASXL2 MUTATED ASXL2 WILD-TYPE
  STAGE I               0               1
  STAGE II              1              36
  STAGE III             3              41
  STAGE IV              4              40
[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              T1+T2 T3 T4
  ASXL2 MUTATED       1  6  2
  ASXL2 WILD-TYPE    30 59 15
D31V4, multiclass
       clus
vv      ASXL2 MUTATED ASXL2 WILD-TYPE
  T1+T2             1              30
  T3                6              59
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  ASXL2 MUTATED    4  1  1  2
  ASXL2 WILD-TYPE 70 12 23  4
D31V5, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  N0             4              70
  N1             1              12
  N2             1              23
  N3             2               4
[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              M0 M1 MX
  ASXL2 MUTATED    5  0  4
  ASXL2 WILD-TYPE 71  4 45
D31V6, multiclass
    clus
vv   ASXL2 MUTATED ASXL2 WILD-TYPE
  M0             5              71
  M1             0               4
  MX             4              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"
D31V7, binary
                 cls
clus               0  1
  ASXL2 MUTATED    2  7
  ASXL2 WILD-TYPE 30 91
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ASXL2 MUTATED      2    7
  ASXL2 WILD-TYPE   30   91
        clus
vv       ASXL2 MUTATED ASXL2 WILD-TYPE
  FEMALE             2              30
  MALE               7              91
[1] 2 2
[1] FALSE
D31V8, continuous
[1] "Remove cluster labels:" "ASXL2 MUTATED"         
clus
  ASXL2 MUTATED ASXL2 WILD-TYPE 
              1              36 
     TCGA-CF-A1HS      TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-DK-A2HX      TCGA-DK-A3IN 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-DK-A3IV      TCGA-DK-A3WX      TCGA-E5-A2PC      TCGA-G2-A2EC 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-G2-A2EF      TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EO 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-GC-A3BM      TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-GC-A3RD      TCGA-GC-A3YS      TCGA-GD-A3OS      TCGA-GV-A3JV 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-GV-A3JW      TCGA-GV-A3JX      TCGA-GV-A3QF      TCGA-GV-A3QH 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" "ASXL2 WILD-TYPE" 
D31V9, continuous
D31V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ASXL2 MUTATED       1                         0     7
  ASXL2 WILD-TYPE     7                         6   100
D31V11, multiclass
                           clus
vv                          ASXL2 MUTATED ASXL2 WILD-TYPE
  ASIAN                                 1               7
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 7             100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = PSIP1 MUTATION ANALYSIS
D32V1, survival
                 sevent
clus2              0  1
  PSIP1 MUTATED    4  3
  PSIP1 WILD-TYPE 76 42
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              7             118 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              3              42 
$`PSIP1 MUTATED`
TCGA-BT-A2LB TCGA-CF-A27C TCGA-DK-A1AG TCGA-DK-A3IS TCGA-FD-A3SO TCGA-FD-A3SS 
        5.59         0.69        15.62        50.27         5.52         1.97 
TCGA-G2-A3VY 
        0.85 

$`PSIP1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PH TCGA-BT-A3PJ 
       14.89        14.96         8.35         3.65         4.67        12.82 
TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 
        2.07        15.42        28.70         1.94         2.93        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        2.04         0.46         0.43        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         5.19        16.31         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A2I6 
       17.62         1.81        10.59         7.79       123.85        87.32 
TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IT 
        2.20         3.98         7.82         8.22        10.49        21.30 
TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 
       20.02         9.67         8.28        10.55       140.81        48.00 
TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 
       43.59        24.66         0.10        12.89         8.94         6.87 
TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL 
        4.01        12.43        11.93        45.93        24.30        22.45 
TCGA-FD-A3SM TCGA-FD-A3SN TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FJ-A3Z7 
        6.12        12.82        13.18        46.78        19.79        15.19 
TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF TCGA-G2-A2EJ 
        3.48         4.08         3.25        22.32        61.94        30.61 
TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE TCGA-GC-A3BM 
        5.69        35.24        17.26         7.04        20.12         2.89 
TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD TCGA-GC-A3WC 
        2.24        15.81         4.50        15.91        14.07        17.75 
TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS TCGA-GU-A42R 
        1.12         7.73         2.10         3.12        20.98        11.31 
TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
        4.41         6.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  PSIP1 MUTATED PSIP1 WILD-TYPE 
           0.69            0.10 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
          50.27          140.81 
  PSIP1 MUTATED PSIP1 WILD-TYPE 
          5.520           9.305 
[1] "0.7 - 50.3 (5.5)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1.8"
D32V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PSIP1 MUTATED         0        2         2        2
  PSIP1 WILD-TYPE       1       35        42       42
D32V3, multiclass
           clus
vv          PSIP1 MUTATED PSIP1 WILD-TYPE
  STAGE I               0               1
  STAGE II              2              35
  STAGE III             2              42
  STAGE IV              2              42
[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              T1+T2 T3 T4
  PSIP1 MUTATED       1  4  1
  PSIP1 WILD-TYPE    30 61 16
D32V4, multiclass
       clus
vv      PSIP1 MUTATED PSIP1 WILD-TYPE
  T1+T2             1              30
  T3                4              61
  T4                1              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  PSIP1 MUTATED    4  1  0  1
  PSIP1 WILD-TYPE 70 12 24  5
D32V5, multiclass
    clus
vv   PSIP1 MUTATED PSIP1 WILD-TYPE
  N0             4              70
  N1             1              12
  N2             0              24
  N3             1               5
[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              M0 M1 MX
  PSIP1 MUTATED    4  0  2
  PSIP1 WILD-TYPE 72  4 47
D32V6, multiclass
    clus
vv   PSIP1 MUTATED PSIP1 WILD-TYPE
  M0             4              72
  M1             0               4
  MX             2              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                 cls
clus               0  1
  PSIP1 MUTATED    1  6
  PSIP1 WILD-TYPE 31 92
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PSIP1 MUTATED      1    6
  PSIP1 WILD-TYPE   31   92
        clus
vv       PSIP1 MUTATED PSIP1 WILD-TYPE
  FEMALE             1              31
  MALE               6              92
[1] 2 2
[1] FALSE
D32V8, continuous
[1] "Remove cluster labels:" "PSIP1 MUTATED"         
clus
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              2              35 
     TCGA-CF-A1HS      TCGA-CF-A3MF      TCGA-CF-A3MG      TCGA-CF-A3MH 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-DK-A2HX      TCGA-DK-A3IN      TCGA-DK-A3IV 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-E5-A2PC      TCGA-G2-A2EC      TCGA-G2-A2EF 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EO      TCGA-G2-A2ES 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-GC-A3BM      TCGA-GC-A3I6 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD      TCGA-GC-A3YS 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GV-A3JV      TCGA-GV-A3JW      TCGA-GV-A3JX 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH      TCGA-GV-A3QI 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
D32V9, continuous
[1] "Remove cluster labels:" "PSIP1 MUTATED"         
clus
  PSIP1 MUTATED PSIP1 WILD-TYPE 
              2              75 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BL-A3JM 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A42B      TCGA-BT-A42C 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-CF-A3MH 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CU-A0YN      TCGA-CU-A0YR      TCGA-CU-A3KJ 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-DK-A1A3      TCGA-DK-A1A5 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-DK-A1A6      TCGA-DK-A1AA      TCGA-DK-A1AC      TCGA-DK-A1AE 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-DK-A2HX      TCGA-DK-A2I6      TCGA-DK-A3IL      TCGA-DK-A3IM 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-DK-A3IN      TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X1      TCGA-FD-A3B3      TCGA-FD-A3B5 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-FD-A3B6      TCGA-FD-A3B7      TCGA-FD-A3B8      TCGA-FD-A3N5 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-FD-A3NA      TCGA-FD-A3SJ      TCGA-FD-A3SM      TCGA-FD-A3SN 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FJ-A3ZE 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-FJ-A3ZF      TCGA-G2-A2EF      TCGA-G2-A2EJ      TCGA-G2-A2ES 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-G2-A3IE      TCGA-GC-A3BM      TCGA-GC-A3RB      TCGA-GC-A3WC 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GD-A2C5      TCGA-GD-A3OQ      TCGA-GD-A3OS 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GU-A42R      TCGA-GV-A3JV      TCGA-GV-A3JX      TCGA-GV-A3JZ 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GV-A3QF      TCGA-GV-A3QG      TCGA-GV-A3QH      TCGA-GV-A3QI 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-GV-A3QK      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-H4-A2HO 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
     TCGA-H4-A2HQ      TCGA-K4-A3WS      TCGA-K4-A3WV 
"PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" "PSIP1 WILD-TYPE" 
D32V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PSIP1 MUTATED       2                         0     5
  PSIP1 WILD-TYPE     6                         6   102
D32V11, multiclass
                           clus
vv                          PSIP1 MUTATED PSIP1 WILD-TYPE
  ASIAN                                 2               6
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 5             102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = ZNF513 MUTATION ANALYSIS
D33V1, survival
                  sevent
clus2               0  1
  ZNF513 MUTATED    5  2
  ZNF513 WILD-TYPE 75 43
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               7              118 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               2               43 
$`ZNF513 MUTATED`
TCGA-BT-A2LB TCGA-BT-A3PH TCGA-DK-A1A3 TCGA-DK-A2I6 TCGA-DK-A3IU TCGA-G2-A3VY 
        5.59         4.67         2.53        87.32        20.02         0.85 
TCGA-GV-A3JW 
        6.41 

$`ZNF513 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LD TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.89        14.96         8.35         3.65        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       15.42        28.70         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.46         0.43         0.69        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A5 TCGA-DK-A1A6 TCGA-DK-A1A7 
        5.46         5.19        16.31         2.14        66.41        18.41 
TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE TCGA-DK-A1AF 
       19.00         8.91       130.88       112.44        16.14        17.62 
TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 TCGA-DK-A3IK 
       15.62         1.81        10.59         7.79       123.85         2.20 
TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IT 
        3.98         7.82         8.22        10.49        50.27        21.30 
TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC 
        9.67         8.28        10.55       140.81        48.00        43.59 
TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 
       24.66         0.10        12.89         8.94         6.87         4.01 
TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SM 
       12.43        11.93        45.93        24.30        22.45         6.12 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       15.19         3.48         4.08         3.25        22.32        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        35.24        17.26         7.04        20.12 
TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC TCGA-GC-A3RD 
        2.89         2.24        15.81         4.50        15.91        14.07 
TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ TCGA-GD-A3OS 
       17.75         1.12         7.73         2.10         3.12        20.98 
TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JX TCGA-GV-A3JZ TCGA-GV-A3QF TCGA-GV-A3QH 
       11.31         4.41         6.15         5.69         7.63         7.79 
TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO TCGA-H4-A2HQ 
        4.14         6.67         6.41        19.07         1.51         6.74 
TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
       38.60         8.75         3.45         4.67 

  ZNF513 MUTATED ZNF513 WILD-TYPE 
            0.85             0.10 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
           87.32           140.81 
  ZNF513 MUTATED ZNF513 WILD-TYPE 
           5.590            9.305 
[1] "0.8 - 87.3 (5.6)"  "0.1 - 140.8 (9.3)"
[1] "hr=" "1"  
D33V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ZNF513 MUTATED         0        3         1        3
  ZNF513 WILD-TYPE       1       34        43       41
D33V3, multiclass
           clus
vv          ZNF513 MUTATED ZNF513 WILD-TYPE
  STAGE I                0                1
  STAGE II               3               34
  STAGE III              1               43
  STAGE IV               3               41
[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               T1+T2 T3 T4
  ZNF513 MUTATED       3  3  0
  ZNF513 WILD-TYPE    28 62 17
D33V4, multiclass
       clus
vv      ZNF513 MUTATED ZNF513 WILD-TYPE
  T1+T2              3               28
  T3                 3               62
  T4                 0               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  ZNF513 MUTATED    2  1  2  0
  ZNF513 WILD-TYPE 72 12 22  6
D33V5, multiclass
    clus
vv   ZNF513 MUTATED ZNF513 WILD-TYPE
  N0              2               72
  N1              1               12
  N2              2               22
  N3              0                6
[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               M0 M1 MX
  ZNF513 MUTATED    4  0  2
  ZNF513 WILD-TYPE 72  4 47
D33V6, multiclass
    clus
vv   ZNF513 MUTATED ZNF513 WILD-TYPE
  M0              4               72
  M1              0                4
  MX              2               47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                  cls
clus                0  1
  ZNF513 MUTATED    1  6
  ZNF513 WILD-TYPE 31 92
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ZNF513 MUTATED      1    6
  ZNF513 WILD-TYPE   31   92
        clus
vv       ZNF513 MUTATED ZNF513 WILD-TYPE
  FEMALE              1               31
  MALE                6               92
[1] 2 2
[1] FALSE
D33V8, continuous
[1] "Remove cluster labels:" "ZNF513 MUTATED"        
clus
  ZNF513 MUTATED ZNF513 WILD-TYPE 
               2               35 
      TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-DK-A2HX       TCGA-DK-A3IN 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-DK-A3IV       TCGA-DK-A3WX       TCGA-E5-A2PC       TCGA-G2-A2EC 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-G2-A2EF       TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EO 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3IE       TCGA-GC-A3BM 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GD-A3OS       TCGA-GV-A3JV       TCGA-GV-A3JX 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH       TCGA-GV-A3QI 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" "ZNF513 WILD-TYPE" 
D33V9, continuous
D33V10, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ZNF513 MUTATED       1                         0     6
  ZNF513 WILD-TYPE     7                         6   101
D33V11, multiclass
                           clus
vv                          ZNF513 MUTATED ZNF513 WILD-TYPE
  ASIAN                                  1                7
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  6              101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = FOXA1 MUTATION ANALYSIS
D34V1, survival
                 sevent
clus2              0  1
  FOXA1 MUTATED    4  3
  FOXA1 WILD-TYPE 76 42
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              7             118 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              3              42 
$`FOXA1 MUTATED`
TCGA-BT-A2LB TCGA-BT-A2LD TCGA-E5-A2PC TCGA-FD-A3SL TCGA-FD-A3SM TCGA-GV-A3QK 
        5.59         3.65        43.59        22.45         6.12         6.67 
TCGA-HQ-A2OE 
       38.60 

$`FOXA1 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A3PH TCGA-BT-A3PJ TCGA-BT-A3PK 
       14.89        14.96         8.35         4.67        12.82         2.07 
TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F1 TCGA-C4-A0F6 TCGA-C4-A0F7 
       15.42        28.70         1.94         2.93        23.01         2.04 
TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO TCGA-CU-A0YR 
        0.46         0.43         0.69        12.92         4.90         7.20 
TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 TCGA-DK-A1A6 
        5.46         5.19        16.31         2.53         2.14        66.41 
TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD TCGA-DK-A1AE 
       18.41        19.00         8.91       130.88       112.44        16.14 
TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 TCGA-DK-A2I4 
       17.62        15.62         1.81        10.59         7.79       123.85 
TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN TCGA-DK-A3IQ 
       87.32         2.20         3.98         7.82         8.22        10.49 
TCGA-DK-A3IS TCGA-DK-A3IT TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       50.27        21.30        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 TCGA-FD-A3B5 
      140.81        48.00        24.66         0.10        12.89         8.94 
TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA TCGA-FD-A3SJ 
        6.87         4.01        12.43        11.93        45.93        24.30 
TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ TCGA-FD-A3SR TCGA-FD-A3SS 
       12.82         5.52        13.18        46.78        19.79         1.97 
TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FJ-A3ZF TCGA-FT-A3EE TCGA-G2-A2EC TCGA-G2-A2EF 
       15.19         3.48         4.08         3.25        22.32        61.94 
TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB TCGA-G2-A3IE 
       30.61         5.69        35.24        17.26         7.04        20.12 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         1.12         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98        11.31         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A40E TCGA-GV-A40G TCGA-H4-A2HO 
        7.63         7.79         4.14         6.41        19.07         1.51 
TCGA-H4-A2HQ TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        6.74         8.75         3.45         4.67 

  FOXA1 MUTATED FOXA1 WILD-TYPE 
           3.65            0.10 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
          43.59          140.81 
  FOXA1 MUTATED FOXA1 WILD-TYPE 
          6.670           8.925 
[1] "3.6 - 43.6 (6.7)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1"  
D34V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FOXA1 MUTATED         0        0         1        5
  FOXA1 WILD-TYPE       1       37        43       39
D34V3, multiclass
           clus
vv          FOXA1 MUTATED FOXA1 WILD-TYPE
  STAGE I               0               1
  STAGE II              0              37
  STAGE III             1              43
  STAGE IV              5              39
[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              T1+T2 T3 T4
  FOXA1 MUTATED       2  3  2
  FOXA1 WILD-TYPE    29 62 15
D34V4, multiclass
       clus
vv      FOXA1 MUTATED FOXA1 WILD-TYPE
  T1+T2             2              29
  T3                3              62
  T4                2              15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                 vv
clus              N0 N1 N2 N3
  FOXA1 MUTATED    1  2  4  0
  FOXA1 WILD-TYPE 73 11 20  6
D34V5, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  N0             1              73
  N1             2              11
  N2             4              20
  N3             0               6
[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              M0 M1 MX
  FOXA1 MUTATED    3  2  2
  FOXA1 WILD-TYPE 73  2 47
D34V6, multiclass
    clus
vv   FOXA1 MUTATED FOXA1 WILD-TYPE
  M0             3              73
  M1             2               2
  MX             2              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                 cls
clus               0  1
  FOXA1 MUTATED    4  3
  FOXA1 WILD-TYPE 28 95
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FOXA1 MUTATED      4    3
  FOXA1 WILD-TYPE   28   95
        clus
vv       FOXA1 MUTATED FOXA1 WILD-TYPE
  FEMALE             4              28
  MALE               3              95
[1] 2 2
[1] FALSE
D34V8, continuous
[1] "Remove cluster labels:" "FOXA1 MUTATED"         
clus
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              2              35 
     TCGA-CF-A1HS      TCGA-CF-A27C      TCGA-CF-A3MF      TCGA-CF-A3MG 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-CF-A3MH      TCGA-CF-A3MI      TCGA-DK-A2HX      TCGA-DK-A3IN 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-DK-A3IV      TCGA-DK-A3WX      TCGA-G2-A2EC      TCGA-G2-A2EF 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-G2-A2EJ      TCGA-G2-A2EK      TCGA-G2-A2EO      TCGA-G2-A2ES 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-G2-A3IB      TCGA-G2-A3IE      TCGA-G2-A3VY      TCGA-GC-A3BM 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GC-A3I6      TCGA-GC-A3OO      TCGA-GC-A3RC      TCGA-GC-A3RD 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GC-A3YS      TCGA-GD-A3OS      TCGA-GV-A3JV      TCGA-GV-A3JW 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GV-A3JX      TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QH 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A40E      TCGA-GV-A40G 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
D34V9, continuous
[1] "Remove cluster labels:" "FOXA1 MUTATED"         
clus
  FOXA1 MUTATED FOXA1 WILD-TYPE 
              2              75 
     TCGA-BL-A0C8      TCGA-BL-A13I      TCGA-BL-A13J      TCGA-BL-A3JM 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-BT-A20J      TCGA-BT-A20N      TCGA-BT-A42B      TCGA-BT-A42C 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-C4-A0F0      TCGA-C4-A0F1      TCGA-C4-A0F6      TCGA-CF-A3MH 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-CF-A3MI      TCGA-CU-A0YN      TCGA-CU-A0YR      TCGA-CU-A3KJ 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-CU-A3QU      TCGA-CU-A3YL      TCGA-DK-A1A3      TCGA-DK-A1A5 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-DK-A1A6      TCGA-DK-A1AA      TCGA-DK-A1AC      TCGA-DK-A1AE 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-DK-A2HX      TCGA-DK-A2I6      TCGA-DK-A3IL      TCGA-DK-A3IM 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-DK-A3IN      TCGA-DK-A3IQ      TCGA-DK-A3IU      TCGA-DK-A3IV 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-DK-A3WX      TCGA-DK-A3X1      TCGA-FD-A3B3      TCGA-FD-A3B5 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-FD-A3B6      TCGA-FD-A3B7      TCGA-FD-A3B8      TCGA-FD-A3N5 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-FD-A3NA      TCGA-FD-A3SJ      TCGA-FD-A3SN      TCGA-FD-A3SO 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-FD-A3SP      TCGA-FD-A3SQ      TCGA-FD-A3SR      TCGA-FD-A3SS 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-FJ-A3ZE      TCGA-FJ-A3ZF      TCGA-G2-A2EF      TCGA-G2-A2EJ 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-G2-A2ES      TCGA-G2-A3IE      TCGA-GC-A3BM      TCGA-GC-A3RB 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GC-A3WC      TCGA-GC-A3YS      TCGA-GD-A2C5      TCGA-GD-A3OQ 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GD-A3OS      TCGA-GU-A42R      TCGA-GV-A3JV      TCGA-GV-A3JX 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GV-A3JZ      TCGA-GV-A3QF      TCGA-GV-A3QG      TCGA-GV-A3QH 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-GV-A3QI      TCGA-GV-A40E      TCGA-GV-A40G      TCGA-H4-A2HO 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
     TCGA-H4-A2HQ      TCGA-K4-A3WS      TCGA-K4-A3WV 
"FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" "FOXA1 WILD-TYPE" 
D34V10, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FOXA1 MUTATED       0                         0     6
  FOXA1 WILD-TYPE     8                         6   101
D34V11, multiclass
                           clus
vv                          FOXA1 MUTATED FOXA1 WILD-TYPE
  ASIAN                                 0               8
  BLACK OR AFRICAN AMERICAN             0               6
  WHITE                                 6             101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = TRIP11 MUTATION ANALYSIS
D35V1, survival
                  sevent
clus2               0  1
  TRIP11 MUTATED    3  2
  TRIP11 WILD-TYPE 77 43
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               5              120 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               2               43 
$`TRIP11 MUTATED`
TCGA-C4-A0F1 TCGA-DK-A3IT TCGA-FD-A3SM TCGA-FJ-A3ZF TCGA-G2-A3IE 
        2.93        21.30         6.12         4.08        20.12 

$`TRIP11 WILD-TYPE`
TCGA-BL-A0C8 TCGA-BL-A13I TCGA-BL-A13J TCGA-BL-A3JM TCGA-BT-A0S7 TCGA-BT-A0YX 
       40.08         7.33         2.66         6.74         6.58        11.93 
TCGA-BT-A20J TCGA-BT-A20N TCGA-BT-A20O TCGA-BT-A20P TCGA-BT-A20Q TCGA-BT-A20R 
       19.04        32.84        12.16        17.88        19.50         5.06 
TCGA-BT-A20T TCGA-BT-A20U TCGA-BT-A20W TCGA-BT-A2LB TCGA-BT-A2LD TCGA-BT-A3PH 
       14.89        14.96         8.35         5.59         3.65         4.67 
TCGA-BT-A3PJ TCGA-BT-A3PK TCGA-BT-A42B TCGA-BT-A42C TCGA-C4-A0F0 TCGA-C4-A0F6 
       12.82         2.07        15.42        28.70         1.94        23.01 
TCGA-C4-A0F7 TCGA-CF-A1HR TCGA-CF-A1HS TCGA-CF-A27C TCGA-CU-A0YN TCGA-CU-A0YO 
        2.04         0.46         0.43         0.69        12.92         4.90 
TCGA-CU-A0YR TCGA-CU-A3KJ TCGA-CU-A3QU TCGA-CU-A3YL TCGA-DK-A1A3 TCGA-DK-A1A5 
        7.20         5.46         5.19        16.31         2.53         2.14 
TCGA-DK-A1A6 TCGA-DK-A1A7 TCGA-DK-A1AA TCGA-DK-A1AB TCGA-DK-A1AC TCGA-DK-A1AD 
       66.41        18.41        19.00         8.91       130.88       112.44 
TCGA-DK-A1AE TCGA-DK-A1AF TCGA-DK-A1AG TCGA-DK-A2HX TCGA-DK-A2I1 TCGA-DK-A2I2 
       16.14        17.62        15.62         1.81        10.59         7.79 
TCGA-DK-A2I4 TCGA-DK-A2I6 TCGA-DK-A3IK TCGA-DK-A3IL TCGA-DK-A3IM TCGA-DK-A3IN 
      123.85        87.32         2.20         3.98         7.82         8.22 
TCGA-DK-A3IQ TCGA-DK-A3IS TCGA-DK-A3IU TCGA-DK-A3IV TCGA-DK-A3WW TCGA-DK-A3WX 
       10.49        50.27        20.02         9.67         8.28        10.55 
TCGA-DK-A3WY TCGA-DK-A3X1 TCGA-E5-A2PC TCGA-E7-A3X6 TCGA-E7-A3Y1 TCGA-FD-A3B3 
      140.81        48.00        43.59        24.66         0.10        12.89 
TCGA-FD-A3B5 TCGA-FD-A3B6 TCGA-FD-A3B7 TCGA-FD-A3B8 TCGA-FD-A3N5 TCGA-FD-A3NA 
        8.94         6.87         4.01        12.43        11.93        45.93 
TCGA-FD-A3SJ TCGA-FD-A3SL TCGA-FD-A3SN TCGA-FD-A3SO TCGA-FD-A3SP TCGA-FD-A3SQ 
       24.30        22.45        12.82         5.52        13.18        46.78 
TCGA-FD-A3SR TCGA-FD-A3SS TCGA-FJ-A3Z7 TCGA-FJ-A3ZE TCGA-FT-A3EE TCGA-G2-A2EC 
       19.79         1.97        15.19         3.48         3.25        22.32 
TCGA-G2-A2EF TCGA-G2-A2EJ TCGA-G2-A2EK TCGA-G2-A2EO TCGA-G2-A2ES TCGA-G2-A3IB 
       61.94        30.61         5.69        35.24        17.26         7.04 
TCGA-G2-A3VY TCGA-GC-A3BM TCGA-GC-A3I6 TCGA-GC-A3OO TCGA-GC-A3RB TCGA-GC-A3RC 
        0.85         2.89         2.24        15.81         4.50        15.91 
TCGA-GC-A3RD TCGA-GC-A3WC TCGA-GC-A3YS TCGA-GD-A2C5 TCGA-GD-A3OP TCGA-GD-A3OQ 
       14.07        17.75         1.12         7.73         2.10         3.12 
TCGA-GD-A3OS TCGA-GU-A42R TCGA-GV-A3JV TCGA-GV-A3JW TCGA-GV-A3JX TCGA-GV-A3JZ 
       20.98        11.31         4.41         6.41         6.15         5.69 
TCGA-GV-A3QF TCGA-GV-A3QH TCGA-GV-A3QI TCGA-GV-A3QK TCGA-GV-A40E TCGA-GV-A40G 
        7.63         7.79         4.14         6.67         6.41        19.07 
TCGA-H4-A2HO TCGA-H4-A2HQ TCGA-HQ-A2OE TCGA-K4-A3WS TCGA-K4-A3WU TCGA-K4-A3WV 
        1.51         6.74        38.60         8.75         3.45         4.67 

  TRIP11 MUTATED TRIP11 WILD-TYPE 
            2.93             0.10 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           21.30           140.81 
  TRIP11 MUTATED TRIP11 WILD-TYPE 
           6.120            8.925 
[1] "2.9 - 21.3 (6.1)"  "0.1 - 140.8 (8.9)"
[1] "hr=" "1.2"
D35V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  TRIP11 MUTATED         0        1         3        1
  TRIP11 WILD-TYPE       1       36        41       43
D35V3, multiclass
           clus
vv          TRIP11 MUTATED TRIP11 WILD-TYPE
  STAGE I                0                1
  STAGE II               1               36
  STAGE III              3               41
  STAGE IV               1               43
[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               T1+T2 T3 T4
  TRIP11 MUTATED       0  3  0
  TRIP11 WILD-TYPE    31 62 17
D35V4, multiclass
       clus
vv      TRIP11 MUTATED TRIP11 WILD-TYPE
  T1+T2              0               31
  T3                 3               62
  T4                 0               17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                  vv
clus               N0 N1 N2 N3
  TRIP11 MUTATED    3  0  1  0
  TRIP11 WILD-TYPE 71 13 23  6
D35V5, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  N0              3               71
  N1              0               13
  N2              1               23
  N3              0                6
[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               M0 M1 MX
  TRIP11 MUTATED    3  1  1
  TRIP11 WILD-TYPE 73  3 48
D35V6, multiclass
    clus
vv   TRIP11 MUTATED TRIP11 WILD-TYPE
  M0              3               73
  M1              1                3
  MX              1               48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                  cls
clus                0  1
  TRIP11 MUTATED    0  5
  TRIP11 WILD-TYPE 32 93
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TRIP11 MUTATED      0    5
  TRIP11 WILD-TYPE   32   93
        clus
vv       TRIP11 MUTATED TRIP11 WILD-TYPE
  FEMALE              0               32
  MALE                5               93
[1] 2 2
[1] FALSE
D35V8, continuous
[1] "Remove cluster labels:" "TRIP11 MUTATED"        
clus
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               1               36 
      TCGA-CF-A1HS       TCGA-CF-A27C       TCGA-CF-A3MF       TCGA-CF-A3MG 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-CF-A3MH       TCGA-CF-A3MI       TCGA-DK-A2HX       TCGA-DK-A3IN 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A3IV       TCGA-DK-A3WX       TCGA-E5-A2PC       TCGA-G2-A2EC 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-G2-A2EF       TCGA-G2-A2EJ       TCGA-G2-A2EK       TCGA-G2-A2EO 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-G2-A2ES       TCGA-G2-A3IB       TCGA-G2-A3VY       TCGA-GC-A3BM 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RC       TCGA-GC-A3RD 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GC-A3YS       TCGA-GD-A3OS       TCGA-GV-A3JV       TCGA-GV-A3JW 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GV-A3JX       TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QH 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GV-A3QI       TCGA-GV-A3QK       TCGA-GV-A40E       TCGA-GV-A40G 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
D35V9, continuous
D35V10, continuous
[1] "Remove cluster labels:" "TRIP11 MUTATED"        
clus
  TRIP11 MUTATED TRIP11 WILD-TYPE 
               2               93 
      TCGA-BL-A0C8       TCGA-BL-A13I       TCGA-BL-A13J       TCGA-BL-A3JM 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-BT-A0S7       TCGA-BT-A0YX       TCGA-BT-A20J       TCGA-BT-A20N 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-BT-A20O       TCGA-BT-A20P       TCGA-BT-A20Q       TCGA-BT-A20T 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-BT-A20W       TCGA-BT-A2LB       TCGA-BT-A2LD       TCGA-BT-A3PH 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-BT-A3PJ       TCGA-BT-A3PK       TCGA-BT-A42B       TCGA-BT-A42C 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-CU-A0YN       TCGA-CU-A0YO       TCGA-CU-A0YR       TCGA-CU-A3KJ 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-CU-A3QU       TCGA-CU-A3YL       TCGA-DK-A1A3       TCGA-DK-A1A5 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A1A6       TCGA-DK-A1A7       TCGA-DK-A1AA       TCGA-DK-A1AB 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A1AC       TCGA-DK-A1AD       TCGA-DK-A1AE       TCGA-DK-A1AF 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A1AG       TCGA-DK-A2HX       TCGA-DK-A2I1       TCGA-DK-A2I2 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A2I4       TCGA-DK-A2I6       TCGA-DK-A3IK       TCGA-DK-A3IL 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A3IM       TCGA-DK-A3IN       TCGA-DK-A3IQ       TCGA-DK-A3IS 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A3IU       TCGA-DK-A3WW       TCGA-DK-A3WX       TCGA-DK-A3WY 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-DK-A3X1       TCGA-E5-A2PC       TCGA-FD-A3B3       TCGA-FD-A3B5 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-FD-A3B6       TCGA-FD-A3B7       TCGA-FD-A3B8       TCGA-FD-A3N5 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-FD-A3NA       TCGA-FD-A3SJ       TCGA-FD-A3SL       TCGA-FD-A3SN 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-FD-A3SO       TCGA-FD-A3SP       TCGA-FD-A3SQ       TCGA-FD-A3SR 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-FD-A3SS       TCGA-FJ-A3Z7       TCGA-FT-A3EE       TCGA-GC-A3BM 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GC-A3I6       TCGA-GC-A3OO       TCGA-GC-A3RB       TCGA-GC-A3RC 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GC-A3RD       TCGA-GC-A3WC       TCGA-GC-A3YS       TCGA-GD-A2C5 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GD-A3OP       TCGA-GD-A3OQ       TCGA-GV-A3JV       TCGA-GV-A3JX 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GV-A3JZ       TCGA-GV-A3QF       TCGA-GV-A3QG       TCGA-GV-A3QI 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-GV-A3QK       TCGA-GV-A40G       TCGA-H4-A2HO       TCGA-K4-A3WS 
"TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" "TRIP11 WILD-TYPE" 
      TCGA-K4-A3WV 
"TRIP11 WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TRIP11 MUTATED       0                         0     4
  TRIP11 WILD-TYPE     8                         6   103
D35V11, multiclass
                           clus
vv                          TRIP11 MUTATED TRIP11 WILD-TYPE
  ASIAN                                  0                8
  BLACK OR AFRICAN AMERICAN              0                6
  WHITE                                  4              103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
