[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"        "-oTREAD-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/READ-TP/11541704/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/10686211/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=69, common to both=69
[1] 12 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           56            13 
  APC MUTATED APC WILD-TYPE 
           56            13 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            44             25 
  TP53 MUTATED TP53 WILD-TYPE 
            44             25 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              9              60 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
  NRAS MUTATED NRAS WILD-TYPE 
             5             64 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               64 
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               64 
[1] "RBM10 MUTATION ANALYSIS"
[1] 3
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              65 
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              65 
[1] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
[1] "CCDC88C MUTATION ANALYSIS"
[1] 3
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                3                66 
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                3                66 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 69 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
         546         1309          412          387           NA           NA 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
         365          974          244          215           31           61 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
          NA           31         1400         1035           NA         1522 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 
         366          184           NA           NA           30          485 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
         608           NA          608          243           30           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
          NA          608           31         1124          518          396 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
        1065          426           31         1461           NA          974 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
         608          853         1096          427           31          518 
TCGA-AG-4015 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          NA          638          424          183          790          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
        1126          485         1096          276          365         2130 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1947          334         1520           NA           NA         1885 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1247         1157         3562 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=44,	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=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'ETHNICITY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
[3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
[5] "PATHOLOGY.M.STAGE"         "GENDER"                   
[7] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
[9] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 69 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 5 14 47  3 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
    5    14    50 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 5 14 47  3 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
    5    14    50 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
43 14 12 
[1] "table(vv)"
vv
N0 N1 N2 
43 14 12 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
43 14 12 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
43 14 12 
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  APC MUTATED   45  6
  APC WILD-TYPE  9  3
  APC MUTATED APC WILD-TYPE 
           51            12 
  APC MUTATED APC WILD-TYPE 
            6             3 
$`APC MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3581 
       43.04        13.55        12.72        10.39         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       50.04        12.03         0.99        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A002 
       19.99        28.04        36.03        14.04         1.02        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01W 
       13.94         6.02        25.97        37.02        36.03        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       41.00        38.04       117.11 

$`APC WILD-TYPE`
TCGA-AF-2689 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       17.95        36.03        12.00        32.02         1.02         6.05 
TCGA-AG-3608 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L 
       15.95        17.03        23.01        15.95         9.07        12.00 

  APC MUTATED APC WILD-TYPE 
         0.99          1.02 
  APC MUTATED APC WILD-TYPE 
       117.11         36.03 
  APC MUTATED APC WILD-TYPE 
        19.99         15.95 
[1] "1.0 - 117.1 (20.0)" "1.0 - 36.0 (15.9)" 
[1] "hr=" "3.3"
D1V2, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  APC MUTATED        17        4        15         4          6          3
  APC WILD-TYPE       1        2         4         0          2          1
               vv
clus            STAGE IV
  APC MUTATED          7
  APC WILD-TYPE        3
D1V3, multiclass
            clus
vv           APC MUTATED APC WILD-TYPE
  STAGE I             17             1
  STAGE II             4             2
  STAGE IIA           15             4
  STAGE III            4             0
  STAGE IIIB           6             2
  STAGE IIIC           3             1
  STAGE IV             7             3
[1] 7 2
[1] 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
  APC MUTATED    5 13    38
  APC WILD-TYPE  0  1    12
D1V4, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  T1              5             0
  T2             13             1
  T3+T4          38            12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
               vv
clus            N0 N1 N2
  APC MUTATED   36 11  9
  APC WILD-TYPE  7  3  3
D1V5, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          36             7
  N1          11             3
  N2           9             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
               cls
clus             0  1
  APC MUTATED   49  7
  APC WILD-TYPE 10  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     49    7
  APC WILD-TYPE   10    3
    clus
vv   APC MUTATED APC WILD-TYPE
  M0          49            10
  M1           7             3
[1] 2 2
[1] FALSE
D1V7, binary
               cls
clus             0  1
  APC MUTATED   25 31
  APC WILD-TYPE  5  8
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     25   31
  APC WILD-TYPE    5    8
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          25             5
  MALE            31             8
[1] 2 2
[1] FALSE
D1V8, binary
               cls
clus             0  1
  APC MUTATED   46  6
  APC WILD-TYPE 11  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     46    6
  APC WILD-TYPE   11    2
                                clus
vv                               APC MUTATED APC WILD-TYPE
  RECTAL ADENOCARCINOMA                   46            11
  RECTAL MUCINOUS ADENOCARCINOMA           6             2
[1] 2 2
[1] FALSE
               vv
clus            R0 R1 R2
  APC MUTATED   48  1  6
  APC WILD-TYPE 11  0  2
D1V9, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          48            11
  R1           1             0
  R2           6             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous

Clustering(2) Variable = TP53 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   36  4
  TP53 WILD-TYPE 18  5
  TP53 MUTATED TP53 WILD-TYPE 
            40             23 
  TP53 MUTATED TP53 WILD-TYPE 
             4              5 
$`TP53 MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3578 
       17.95        43.04        12.72        10.39        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 
        7.07        46.03         2.01        50.04         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 
       19.99        19.99         7.99        19.99        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       14.04         1.02        17.03         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 
       15.95         9.07        70.03        64.01        10.98         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

$`TP53 WILD-TYPE`
TCGA-AF-2692 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       13.55        36.03         8.02         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3878 
        1.02        34.03        12.03         6.05         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 
        1.02        36.95        13.02        14.01        20.98        13.94 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A025 TCGA-AG-A02G 
       25.97        36.03        12.00        49.97        38.96 

  TP53 MUTATED TP53 WILD-TYPE 
          0.99           0.99 
  TP53 MUTATED TP53 WILD-TYPE 
        117.11          49.97 
  TP53 MUTATED TP53 WILD-TYPE 
         19.99          13.55 
[1] "1.0 - 117.1 (20.0)" "1.0 - 50.0 (13.6)" 
[1] "hr=" "2.9"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  TP53 MUTATED         9        5        13         2          6          3
  TP53 WILD-TYPE       9        1         6         2          2          1
                vv
clus             STAGE IV
  TP53 MUTATED          6
  TP53 WILD-TYPE        4
D2V3, multiclass
            clus
vv           TP53 MUTATED TP53 WILD-TYPE
  STAGE I               9              9
  STAGE II              5              1
  STAGE IIA            13              6
  STAGE III             2              2
  STAGE IIIB            6              2
  STAGE IIIC            3              1
  STAGE IV              6              4
[1] 7 2
[1] 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    1  8    35
  TP53 WILD-TYPE  4  6    15
D2V4, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               1              4
  T2               8              6
  T3+T4           35             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
  TP53 MUTATED   27  9  8
  TP53 WILD-TYPE 16  5  4
D2V5, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           27             16
  N1            9              5
  N2            8              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                cls
clus              0  1
  TP53 MUTATED   38  6
  TP53 WILD-TYPE 21  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     38    6
  TP53 WILD-TYPE   21    4
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           38             21
  M1            6              4
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus              0  1
  TP53 MUTATED   19 25
  TP53 WILD-TYPE 11 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19   25
  TP53 WILD-TYPE   11   14
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           19             11
  MALE             25             14
[1] 2 2
[1] FALSE
D2V8, binary
                cls
clus              0  1
  TP53 MUTATED   40  4
  TP53 WILD-TYPE 17  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     40    4
  TP53 WILD-TYPE   17    4
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  RECTAL ADENOCARCINOMA                    40             17
  RECTAL MUCINOUS ADENOCARCINOMA            4              4
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  TP53 MUTATED   39  1  4
  TP53 WILD-TYPE 20  0  4
D2V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           39             20
  R1            1              0
  R2            4              4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous

Clustering(3) Variable = KRAS MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   32  3
  KRAS WILD-TYPE 22  6
  KRAS MUTATED KRAS WILD-TYPE 
            35             28 
  KRAS MUTATED KRAS WILD-TYPE 
             3              6 
$`KRAS MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       17.95        43.04        13.55        12.00         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        2.01         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 
        7.99         0.99         0.99        36.95        13.02         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 
       32.02        19.99        28.04        14.04        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01W 
        6.02        25.97        23.01        15.95        36.03        70.03 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97        61.97        41.00        38.04 

$`KRAS WILD-TYPE`
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       12.72        10.39        36.03        32.02         1.02        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       46.03        34.03         6.05        15.95        19.99        19.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       19.99         1.02        17.03        35.01        14.01        48.03 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L 
       36.03         1.02        20.98        37.02         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 
       64.01         1.94        38.96       117.11 

  KRAS MUTATED KRAS WILD-TYPE 
          0.99           1.02 
  KRAS MUTATED KRAS WILD-TYPE 
         70.03         117.11 
  KRAS MUTATED KRAS WILD-TYPE 
         14.04          19.99 
[1] "1.0 - 70.0 (14.0)"  "1.0 - 117.1 (20.0)"
[1] "hr=" "2.3"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  KRAS MUTATED        13        3         9         3          4          2
  KRAS WILD-TYPE       5        3        10         1          4          2
                vv
clus             STAGE IV
  KRAS MUTATED          4
  KRAS WILD-TYPE        6
D3V3, multiclass
            clus
vv           KRAS MUTATED KRAS WILD-TYPE
  STAGE I              13              5
  STAGE II              3              3
  STAGE IIA             9             10
  STAGE III             3              1
  STAGE IIIB            4              4
  STAGE IIIC            2              2
  STAGE IV              4              6
[1] 7 2
[1] 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
  KRAS MUTATED    5  8    25
  KRAS WILD-TYPE  0  6    25
D3V4, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               5              0
  T2               8              6
  T3+T4           25             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                vv
clus             N0 N1 N2
  KRAS MUTATED   25  7  6
  KRAS WILD-TYPE 18  7  6
D3V5, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           25             18
  N1            7              7
  N2            6              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                cls
clus              0  1
  KRAS MUTATED   34  4
  KRAS WILD-TYPE 25  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     34    4
  KRAS WILD-TYPE   25    6
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0           34             25
  M1            4              6
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus              0  1
  KRAS MUTATED   19 19
  KRAS WILD-TYPE 11 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     19   19
  KRAS WILD-TYPE   11   20
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           19             11
  MALE             19             20
[1] 2 2
[1] FALSE
D3V8, binary
                cls
clus              0  1
  KRAS MUTATED   29  6
  KRAS WILD-TYPE 28  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     29    6
  KRAS WILD-TYPE   28    2
                                clus
vv                               KRAS MUTATED KRAS WILD-TYPE
  RECTAL ADENOCARCINOMA                    29             28
  RECTAL MUCINOUS ADENOCARCINOMA            6              2
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  KRAS MUTATED   36  0  2
  KRAS WILD-TYPE 23  1  6
D3V9, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           36             23
  R1            0              1
  R2            2              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous

Clustering(4) Variable = SMAD4 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED    7  0
  SMAD4 WILD-TYPE 47  9
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              7              56 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              0               9 
$`SMAD4 MUTATED`
TCGA-AG-3887 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 
       36.95        14.04        13.94        37.02         9.07        10.98 
TCGA-AG-A02X 
       41.00 

$`SMAD4 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 
        7.99         0.99         0.99        19.99         1.02        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       19.99        28.04        36.03         1.02        17.03        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L 
        6.02        25.97        23.01        15.95        36.03        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       70.03        64.01        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AG-A036 
       38.04       117.11 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           9.07            0.99 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          41.00          117.11 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          14.04           17.49 
[1] "9.1 - 41.0 (14.0)"  "1.0 - 117.1 (17.5)"
[1] "hr="     "8.2e+07"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  SMAD4 MUTATED         2        0         2         1          1          0
  SMAD4 WILD-TYPE      16        6        17         3          7          4
                 vv
clus              STAGE IV
  SMAD4 MUTATED          2
  SMAD4 WILD-TYPE        8
D4V3, multiclass
            clus
vv           SMAD4 MUTATED SMAD4 WILD-TYPE
  STAGE I                2              16
  STAGE II               0               6
  STAGE IIA              2              17
  STAGE III              1               3
  STAGE IIIB             1               7
  STAGE IIIC             0               4
  STAGE IV               2               8
[1] 7 2
[1] 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
  SMAD4 MUTATED    0  2     6
  SMAD4 WILD-TYPE  5 12    44
D4V4, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                0               5
  T2                2              12
  T3+T4             6              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"
                 vv
clus              N0 N1 N2
  SMAD4 MUTATED    4  2  2
  SMAD4 WILD-TYPE 39 12 10
D4V5, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             4              39
  N1             2              12
  N2             2              10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                 cls
clus               0  1
  SMAD4 MUTATED    6  2
  SMAD4 WILD-TYPE 53  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      6    2
  SMAD4 WILD-TYPE   53    8
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  M0             6              53
  M1             2               8
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus               0  1
  SMAD4 MUTATED    3  5
  SMAD4 WILD-TYPE 27 34
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      3    5
  SMAD4 WILD-TYPE   27   34
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE             3              27
  MALE               5              34
[1] 2 2
[1] FALSE
D4V8, binary
                 cls
clus               0  1
  SMAD4 MUTATED    4  4
  SMAD4 WILD-TYPE 53  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED      4    4
  SMAD4 WILD-TYPE   53    4
                                clus
vv                               SMAD4 MUTATED SMAD4 WILD-TYPE
  RECTAL ADENOCARCINOMA                      4              53
  RECTAL MUCINOUS ADENOCARCINOMA             4               4
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  SMAD4 MUTATED    7  0  1
  SMAD4 WILD-TYPE 52  1  7
D4V9, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0             7              52
  R1             0               1
  R2             1               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"
D4V10, continuous

Clustering(5) Variable = FBXW7 MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    7  1
  FBXW7 WILD-TYPE 47  8
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              8              55 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              1               8 
$`FBXW7 MUTATED`
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
        2.01         6.05        15.95        13.02        48.03        20.98 
TCGA-AG-A011 TCGA-AG-A02N 
       37.02        61.97 

$`FBXW7 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        0.99        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 
      117.11 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           2.01            0.99 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          61.97          117.11 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         18.465          17.030 
[1] "2.0 - 62.0 (18.5)"  "1.0 - 117.1 (17.0)"
[1] "hr=" "1.4"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  FBXW7 MUTATED         2        1         5         0          0          1
  FBXW7 WILD-TYPE      16        5        14         4          8          3
                 vv
clus              STAGE IV
  FBXW7 MUTATED          0
  FBXW7 WILD-TYPE       10
D5V3, multiclass
            clus
vv           FBXW7 MUTATED FBXW7 WILD-TYPE
  STAGE I                2              16
  STAGE II               1               5
  STAGE IIA              5              14
  STAGE III              0               4
  STAGE IIIB             0               8
  STAGE IIIC             1               3
  STAGE IV               0              10
[1] 7 2
[1] 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    1  1     7
  FBXW7 WILD-TYPE  4 13    43
D5V4, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T1                1               4
  T2                1              13
  T3+T4             7              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"
                 vv
clus              N0 N1 N2
  FBXW7 MUTATED    8  0  1
  FBXW7 WILD-TYPE 35 14 11
D5V5, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             8              35
  N1             0              14
  N2             1              11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                 cls
clus               0  1
  FBXW7 MUTATED    9  0
  FBXW7 WILD-TYPE 50 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      9    0
  FBXW7 WILD-TYPE   50   10
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  M0             9              50
  M1             0              10
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus               0  1
  FBXW7 MUTATED    3  6
  FBXW7 WILD-TYPE 27 33
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      3    6
  FBXW7 WILD-TYPE   27   33
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE             3              27
  MALE               6              33
[1] 2 2
[1] FALSE
D5V8, binary
                 cls
clus               0  1
  FBXW7 MUTATED    7  1
  FBXW7 WILD-TYPE 50  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED      7    1
  FBXW7 WILD-TYPE   50    7
                                clus
vv                               FBXW7 MUTATED FBXW7 WILD-TYPE
  RECTAL ADENOCARCINOMA                      7              50
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  FBXW7 MUTATED    8  0  0
  FBXW7 WILD-TYPE 51  1  8
D5V9, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0             8              51
  R1             0               1
  R2             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous

Clustering(6) Variable = NRAS MUTATION ANALYSIS
D6V1, survival
                sevent
clus2             0  1
  NRAS MUTATED    4  1
  NRAS WILD-TYPE 50  8
  NRAS MUTATED NRAS WILD-TYPE 
             5             58 
  NRAS MUTATED NRAS WILD-TYPE 
             1              8 
$`NRAS MUTATED`
TCGA-AF-2691 TCGA-AF-3913 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A01L 
       43.04        10.39        13.02        14.01        12.00 

$`NRAS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       17.95        13.55        12.72        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  NRAS MUTATED NRAS WILD-TYPE 
         10.39           0.99 
  NRAS MUTATED NRAS WILD-TYPE 
         43.04         117.11 
  NRAS MUTATED NRAS WILD-TYPE 
         13.02          18.97 
[1] "10.4 - 43.0 (13.0)" "1.0 - 117.1 (19.0)"
[1] "hr=" "1.5"
D6V2, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  NRAS MUTATED         2        0         1         0          1          0
  NRAS WILD-TYPE      16        6        18         4          7          4
                vv
clus             STAGE IV
  NRAS MUTATED          1
  NRAS WILD-TYPE        9
D6V3, multiclass
            clus
vv           NRAS MUTATED NRAS WILD-TYPE
  STAGE I               2             16
  STAGE II              0              6
  STAGE IIA             1             18
  STAGE III             0              4
  STAGE IIIB            1              7
  STAGE IIIC            0              4
  STAGE IV              1              9
[1] 7 2
[1] 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
  NRAS MUTATED    2  0     3
  NRAS WILD-TYPE  3 14    47
D6V4, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T1               2              3
  T2               0             14
  T3+T4            3             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"
                vv
clus             N0 N1 N2
  NRAS MUTATED    3  2  0
  NRAS WILD-TYPE 40 12 12
D6V5, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            3             40
  N1            2             12
  N2            0             12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                cls
clus              0  1
  NRAS MUTATED    4  1
  NRAS WILD-TYPE 55  9
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      4    1
  NRAS WILD-TYPE   55    9
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  M0            4             55
  M1            1              9
[1] 2 2
[1] FALSE
D6V7, binary
                cls
clus              0  1
  NRAS MUTATED    2  3
  NRAS WILD-TYPE 28 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      2    3
  NRAS WILD-TYPE   28   36
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            2             28
  MALE              3             36
[1] 2 2
[1] FALSE
D6V8, binary
                cls
clus              0  1
  NRAS MUTATED    5  0
  NRAS WILD-TYPE 52  8
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      5    0
  NRAS WILD-TYPE   52    8
                                clus
vv                               NRAS MUTATED NRAS WILD-TYPE
  RECTAL ADENOCARCINOMA                     5             52
  RECTAL MUCINOUS ADENOCARCINOMA            0              8
[1] 2 2
[1] FALSE
                vv
clus             R0 R1 R2
  NRAS MUTATED    5  0  0
  NRAS WILD-TYPE 54  1  8
D6V9, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0            5             54
  R1            0              1
  R2            0              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous

Clustering(7) Variable = ARID1A MUTATION ANALYSIS
D7V1, survival
                  sevent
clus2               0  1
  ARID1A MUTATED    4  1
  ARID1A WILD-TYPE 50  8
  ARID1A MUTATED ARID1A WILD-TYPE 
               5               58 
  ARID1A MUTATED ARID1A WILD-TYPE 
               1                8 
$`ARID1A MUTATED`
TCGA-AG-3574 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-A00H TCGA-AG-A025 
       36.03         0.99        13.02        25.97        49.97 

$`ARID1A WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 
       17.95        43.04        13.55        12.72        10.39        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        64.01        10.98         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       61.97        41.00        38.04       117.11 

  ARID1A MUTATED ARID1A WILD-TYPE 
            0.99             0.99 
  ARID1A MUTATED ARID1A WILD-TYPE 
           49.97           117.11 
  ARID1A MUTATED ARID1A WILD-TYPE 
           25.97            17.03 
[1] "1.0 - 50.0 (26.0)"  "1.0 - 117.1 (17.0)"
[1] "hr=" "1.3"
D7V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  ARID1A MUTATED         3        1         1         0          0          0
  ARID1A WILD-TYPE      15        5        18         4          8          4
                  vv
clus               STAGE IV
  ARID1A MUTATED          0
  ARID1A WILD-TYPE       10
D7V3, multiclass
            clus
vv           ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                 3               15
  STAGE II                1                5
  STAGE IIA               1               18
  STAGE III               0                4
  STAGE IIIB              0                8
  STAGE IIIC              0                4
  STAGE IV                0               10
[1] 7 2
[1] 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    2  1     2
  ARID1A WILD-TYPE  3 13    48
D7V4, multiclass
       clus
vv      ARID1A MUTATED ARID1A WILD-TYPE
  T1                 2                3
  T2                 1               13
  T3+T4              2               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"
                  vv
clus               N0 N1 N2
  ARID1A MUTATED    5  0  0
  ARID1A WILD-TYPE 38 14 12
D7V5, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  N0              5               38
  N1              0               14
  N2              0               12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 54 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   54   10
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0              5               54
  M1              0               10
[1] 2 2
[1] FALSE
D7V7, binary
                  cls
clus                0  1
  ARID1A MUTATED    3  2
  ARID1A WILD-TYPE 27 37
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      3    2
  ARID1A WILD-TYPE   27   37
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              3               27
  MALE                2               37
[1] 2 2
[1] FALSE
D7V8, binary
                  cls
clus                0  1
  ARID1A MUTATED    5  0
  ARID1A WILD-TYPE 52  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      5    0
  ARID1A WILD-TYPE   52    8
                                clus
vv                               ARID1A MUTATED ARID1A WILD-TYPE
  RECTAL ADENOCARCINOMA                       5               52
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2
  ARID1A MUTATED    5  0  0
  ARID1A WILD-TYPE 54  1  8
D7V9, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  R0              5               54
  R1              0                1
  R2              0                8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous

Clustering(8) Variable = RBM10 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  RBM10 MUTATED    2  2
  RBM10 WILD-TYPE 52  7
  RBM10 MUTATED RBM10 WILD-TYPE 
              4              59 
  RBM10 MUTATED RBM10 WILD-TYPE 
              2               7 
$`RBM10 MUTATED`
TCGA-AF-2689 TCGA-AG-3583 TCGA-AG-3902 TCGA-AG-3999 
       17.95         2.01        32.02        28.04 

$`RBM10 WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       43.04        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       35.01        14.01         1.02        48.03        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  RBM10 MUTATED RBM10 WILD-TYPE 
           2.01            0.99 
  RBM10 MUTATED RBM10 WILD-TYPE 
          32.02          117.11 
  RBM10 MUTATED RBM10 WILD-TYPE 
         22.995          17.030 
[1] "2.0 - 32.0 (23.0)"  "1.0 - 117.1 (17.0)"
[1] "hr=" "5"  
D8V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  RBM10 MUTATED         0        0         1         0          0          1
  RBM10 WILD-TYPE      18        6        18         4          8          3
                 vv
clus              STAGE IV
  RBM10 MUTATED          2
  RBM10 WILD-TYPE        8
D8V3, multiclass
            clus
vv           RBM10 MUTATED RBM10 WILD-TYPE
  STAGE I                0              18
  STAGE II               0               6
  STAGE IIA              1              18
  STAGE III              0               4
  STAGE IIIB             0               8
  STAGE IIIC             1               3
  STAGE IV               2               8
[1] 7 2
[1] 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
  RBM10 MUTATED    0  0     4
  RBM10 WILD-TYPE  5 14    46
D8V4, multiclass
       clus
vv      RBM10 MUTATED RBM10 WILD-TYPE
  T1                0               5
  T2                0              14
  T3+T4             4              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"
                 vv
clus              N0 N1 N2
  RBM10 MUTATED    1  0  3
  RBM10 WILD-TYPE 42 14  9
D8V5, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  N0             1              42
  N1             0              14
  N2             3               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                 cls
clus               0  1
  RBM10 MUTATED    2  2
  RBM10 WILD-TYPE 57  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE   57    8
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  M0             2              57
  M1             2               8
[1] 2 2
[1] FALSE
D8V7, binary
                 cls
clus               0  1
  RBM10 MUTATED    2  2
  RBM10 WILD-TYPE 28 37
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      2    2
  RBM10 WILD-TYPE   28   37
        clus
vv       RBM10 MUTATED RBM10 WILD-TYPE
  FEMALE             2              28
  MALE               2              37
[1] 2 2
[1] FALSE
D8V8, binary
                 cls
clus               0  1
  RBM10 MUTATED    3  1
  RBM10 WILD-TYPE 54  7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  RBM10 MUTATED      3    1
  RBM10 WILD-TYPE   54    7
                                clus
vv                               RBM10 MUTATED RBM10 WILD-TYPE
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             1               7
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  RBM10 MUTATED    3  0  1
  RBM10 WILD-TYPE 56  1  7
D8V9, multiclass
    clus
vv   RBM10 MUTATED RBM10 WILD-TYPE
  R0             3              56
  R1             0               1
  R2             1               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"
D8V10, continuous

Clustering(9) Variable = TCF7L2 MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  TCF7L2 MUTATED    6  1
  TCF7L2 WILD-TYPE 48  8
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               56 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               1                8 
$`TCF7L2 MUTATED`
TCGA-AF-2692 TCGA-AG-3582 TCGA-AG-3726 TCGA-AG-3882 TCGA-AG-3898 TCGA-AG-4007 
       13.55         1.02         7.99        19.99        48.03         1.02 
TCGA-AG-A032 
       38.04 

$`TCF7L2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       17.95        43.04        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3878 
        0.99        15.95        19.99        19.99         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       37.02        15.95        36.03         9.07        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A036 
       41.00       117.11 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            1.02             0.99 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           48.03           117.11 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           13.55            17.49 
[1] "1.0 - 48.0 (13.6)"  "1.0 - 117.1 (17.5)"
[1] "hr=" "1.2"
D9V2, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  TCF7L2 MUTATED         2        0         2         0          1          0
  TCF7L2 WILD-TYPE      16        6        17         4          7          4
                  vv
clus               STAGE IV
  TCF7L2 MUTATED          2
  TCF7L2 WILD-TYPE        8
D9V3, multiclass
            clus
vv           TCF7L2 MUTATED TCF7L2 WILD-TYPE
  STAGE I                 2               16
  STAGE II                0                6
  STAGE IIA               2               17
  STAGE III               0                4
  STAGE IIIB              1                7
  STAGE IIIC              0                4
  STAGE IV                2                8
[1] 7 2
[1] 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
  TCF7L2 MUTATED    0  2     5
  TCF7L2 WILD-TYPE  5 12    45
D9V4, multiclass
       clus
vv      TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1                 0                5
  T2                 2               12
  T3+T4              5               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"
                  vv
clus               N0 N1 N2
  TCF7L2 MUTATED    4  2  1
  TCF7L2 WILD-TYPE 39 12 11
D9V5, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0              4               39
  N1              2               12
  N2              1               11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    5  2
  TCF7L2 WILD-TYPE 54  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      5    2
  TCF7L2 WILD-TYPE   54    8
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  M0              5               54
  M1              2                8
[1] 2 2
[1] FALSE
D9V7, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    3  4
  TCF7L2 WILD-TYPE 27 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      3    4
  TCF7L2 WILD-TYPE   27   35
        clus
vv       TCF7L2 MUTATED TCF7L2 WILD-TYPE
  FEMALE              3               27
  MALE                4               35
[1] 2 2
[1] FALSE
D9V8, binary
                  cls
clus                0  1
  TCF7L2 MUTATED    6  0
  TCF7L2 WILD-TYPE 51  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  TCF7L2 MUTATED      6    0
  TCF7L2 WILD-TYPE   51    8
                                clus
vv                               TCF7L2 MUTATED TCF7L2 WILD-TYPE
  RECTAL ADENOCARCINOMA                       6               51
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
[1] 2 2
[1] FALSE
                  vv
clus               R0 R1 R2
  TCF7L2 MUTATED    5  0  2
  TCF7L2 WILD-TYPE 54  1  6
D9V9, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0              5               54
  R1              0                1
  R2              2                6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous

Clustering(10) Variable = ERBB2 MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  ERBB2 MUTATED    4  0
  ERBB2 WILD-TYPE 50  9
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              59 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              0               9 
$`ERBB2 MUTATED`
TCGA-AG-3599 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-A00Y 
       12.03        48.03        32.02        23.01 

$`ERBB2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
       13.02        35.01        14.01         1.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04         1.02        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        64.01        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.96        61.97        41.00        38.04       117.11 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
          12.03            0.99 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          48.03          117.11 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         27.515          17.030 
[1] "12.0 - 48.0 (27.5)" "1.0 - 117.1 (17.0)"
[1] "hr="     "7.5e+07"
D10V2, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  ERBB2 MUTATED         1        0         3         0          0          0
  ERBB2 WILD-TYPE      17        6        16         4          8          4
                 vv
clus              STAGE IV
  ERBB2 MUTATED          0
  ERBB2 WILD-TYPE       10
D10V3, multiclass
            clus
vv           ERBB2 MUTATED ERBB2 WILD-TYPE
  STAGE I                1              17
  STAGE II               0               6
  STAGE IIA              3              16
  STAGE III              0               4
  STAGE IIIB             0               8
  STAGE IIIC             0               4
  STAGE IV               0              10
[1] 7 2
[1] 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
  ERBB2 MUTATED    0  1     3
  ERBB2 WILD-TYPE  5 13    47
D10V4, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  T1                0               5
  T2                1              13
  T3+T4             3              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"
                 vv
clus              N0 N1 N2
  ERBB2 MUTATED    4  0  0
  ERBB2 WILD-TYPE 39 14 12
D10V5, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             4              39
  N1             0              14
  N2             0              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                 cls
clus               0  1
  ERBB2 MUTATED    4  0
  ERBB2 WILD-TYPE 55 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      4    0
  ERBB2 WILD-TYPE   55   10
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  M0             4              55
  M1             0              10
[1] 2 2
[1] FALSE
D10V7, binary
                 cls
clus               0  1
  ERBB2 MUTATED    0  4
  ERBB2 WILD-TYPE 30 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      0    4
  ERBB2 WILD-TYPE   30   35
        clus
vv       ERBB2 MUTATED ERBB2 WILD-TYPE
  FEMALE             0              30
  MALE               4              35
[1] 2 2
[1] FALSE
D10V8, binary
                 cls
clus               0  1
  ERBB2 MUTATED    3  0
  ERBB2 WILD-TYPE 54  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ERBB2 MUTATED      3    0
  ERBB2 WILD-TYPE   54    8
                                clus
vv                               ERBB2 MUTATED ERBB2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      3              54
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
[1] 2 2
[1] FALSE
                 vv
clus              R0 R1 R2
  ERBB2 MUTATED    4  0  0
  ERBB2 WILD-TYPE 55  1  8
D10V9, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             4              55
  R1             0               1
  R2             0               8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous

Clustering(11) Variable = KIAA1804 MUTATION ANALYSIS
D11V1, survival
                    sevent
clus2                 0  1
  KIAA1804 MUTATED    7  1
  KIAA1804 WILD-TYPE 47  8
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 8                 55 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 1                  8 
$`KIAA1804 MUTATED`
TCGA-AF-2691 TCGA-AG-3582 TCGA-AG-3598 TCGA-AG-3727 TCGA-AG-3898 TCGA-AG-A002 
       43.04         1.02        50.04         0.99        48.03        20.98 
TCGA-AG-A008 TCGA-AG-A02N 
       13.94        61.97 

$`KIAA1804 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3575 
       17.95        13.55        12.72        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03        34.03         2.01        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        19.99         7.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        17.03         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AG-A036 
      117.11 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.99               0.99 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             61.97             117.11 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             32.01              17.03 
[1] "1.0 - 62.0 (32.0)"  "1.0 - 117.1 (17.0)"
[1] "hr=" "1.6"
D11V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  KIAA1804 MUTATED         3        1         2         1          0          1
  KIAA1804 WILD-TYPE      15        5        17         3          8          3
                    vv
clus                 STAGE IV
  KIAA1804 MUTATED          1
  KIAA1804 WILD-TYPE        9
D11V3, multiclass
            clus
vv           KIAA1804 MUTATED KIAA1804 WILD-TYPE
  STAGE I                   3                 15
  STAGE II                  1                  5
  STAGE IIA                 2                 17
  STAGE III                 1                  3
  STAGE IIIB                0                  8
  STAGE IIIC                1                  3
  STAGE IV                  1                  9
[1] 7 2
[1] 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
  KIAA1804 MUTATED    1  2     6
  KIAA1804 WILD-TYPE  4 12    44
D11V4, multiclass
       clus
vv      KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                   1                  4
  T2                   2                 12
  T3+T4                6                 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"
                    vv
clus                 N0 N1 N2
  KIAA1804 MUTATED    6  2  1
  KIAA1804 WILD-TYPE 37 12 11
D11V5, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0                6                 37
  N1                2                 12
  N2                1                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    8  1
  KIAA1804 WILD-TYPE 51  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      8    1
  KIAA1804 WILD-TYPE   51    9
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  M0                8                 51
  M1                1                  9
[1] 2 2
[1] FALSE
D11V7, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    4  5
  KIAA1804 WILD-TYPE 26 34
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      4    5
  KIAA1804 WILD-TYPE   26   34
        clus
vv       KIAA1804 MUTATED KIAA1804 WILD-TYPE
  FEMALE                4                 26
  MALE                  5                 34
[1] 2 2
[1] FALSE
D11V8, binary
                    cls
clus                  0  1
  KIAA1804 MUTATED    8  1
  KIAA1804 WILD-TYPE 49  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1804 MUTATED      8    1
  KIAA1804 WILD-TYPE   49    7
                                clus
vv                               KIAA1804 MUTATED KIAA1804 WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                 49
  RECTAL MUCINOUS ADENOCARCINOMA                1                  7
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2
  KIAA1804 MUTATED    8  0  1
  KIAA1804 WILD-TYPE 51  1  7
D11V9, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0                8                 51
  R1                0                  1
  R2                1                  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"
D11V10, continuous

Clustering(12) Variable = CCDC88C MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  CCDC88C MUTATED    3  0
  CCDC88C WILD-TYPE 51  9
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                3                60 
  CCDC88C MUTATED CCDC88C WILD-TYPE 
                0                 9 
$`CCDC88C MUTATED`
TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-A036 
        7.99         0.99       117.11 

$`CCDC88C WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
       17.95        43.04        13.55        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         9.07        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 

  CCDC88C MUTATED CCDC88C WILD-TYPE 
             0.99              0.99 
  CCDC88C MUTATED CCDC88C WILD-TYPE 
           117.11             70.03 
  CCDC88C MUTATED CCDC88C WILD-TYPE 
             7.99             17.49 
[1] "1.0 - 117.1 (8.0)" "1.0 - 70.0 (17.5)"
[1] "hr="     "2.6e+07"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  CCDC88C MUTATED         2        0         0         1          0          0
  CCDC88C WILD-TYPE      16        6        19         3          8          4
                   vv
clus                STAGE IV
  CCDC88C MUTATED          0
  CCDC88C WILD-TYPE       10
D12V3, multiclass
            clus
vv           CCDC88C MUTATED CCDC88C WILD-TYPE
  STAGE I                  2                16
  STAGE II                 0                 6
  STAGE IIA                0                19
  STAGE III                1                 3
  STAGE IIIB               0                 8
  STAGE IIIC               0                 4
  STAGE IV                 0                10
[1] 7 2
[1] 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
  CCDC88C MUTATED    0  2     1
  CCDC88C WILD-TYPE  5 12    49
D12V4, multiclass
       clus
vv      CCDC88C MUTATED CCDC88C WILD-TYPE
  T1                  0                 5
  T2                  2                12
  T3+T4               1                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"
                   vv
clus                N0 N1 N2
  CCDC88C MUTATED    2  0  1
  CCDC88C WILD-TYPE 41 14 11
D12V5, multiclass
    clus
vv   CCDC88C MUTATED CCDC88C WILD-TYPE
  N0               2                41
  N1               0                14
  N2               1                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                 0  1
  CCDC88C MUTATED    3  0
  CCDC88C WILD-TYPE 56 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88C MUTATED      3    0
  CCDC88C WILD-TYPE   56   10
    clus
vv   CCDC88C MUTATED CCDC88C WILD-TYPE
  M0               3                56
  M1               0                10
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                 0  1
  CCDC88C MUTATED    1  2
  CCDC88C WILD-TYPE 29 37
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88C MUTATED      1    2
  CCDC88C WILD-TYPE   29   37
        clus
vv       CCDC88C MUTATED CCDC88C WILD-TYPE
  FEMALE               1                29
  MALE                 2                37
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                 0  1
  CCDC88C MUTATED    3  0
  CCDC88C WILD-TYPE 54  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC88C MUTATED      3    0
  CCDC88C WILD-TYPE   54    8
                                clus
vv                               CCDC88C MUTATED CCDC88C WILD-TYPE
  RECTAL ADENOCARCINOMA                        3                54
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2
  CCDC88C MUTATED    3  0  0
  CCDC88C WILD-TYPE 56  1  8
D12V9, multiclass
    clus
vv   CCDC88C MUTATED CCDC88C WILD-TYPE
  R0               3                56
  R1               0                 1
  R2               0                 8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
