
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/Clusters2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Clusters_onlysig.81.4078/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/376907/READ-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/READ-TP/2844265/1.GDAC_clinicalDataPicker.Finished/READ-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=168, in cluster file=69, common to both=69
[1] "Reduce the number of clustering variables from 17 to 16."
[1] 16 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           57            12 
  APC MUTATED APC WILD-TYPE 
           57            12 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              61 
[1] "KIAA1804 MUTATION ANALYSIS"
[1] 3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 9                 60 
[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] "TCF7L2 MUTATION ANALYSIS"
[1] 3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               7               62 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               7               62 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               7               62 
[1] "OPCML MUTATION ANALYSIS"
[1] 3
  OPCML MUTATED OPCML WILD-TYPE 
              6              63 
  OPCML MUTATED OPCML WILD-TYPE 
              6              63 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              5              64 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              5              64 
[1] "SPATA8 MUTATION ANALYSIS"
[1] 3
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               3               66 
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               3               66 
[1] "ERBB2 MUTATION ANALYSIS"
[1] 3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              4              65 
[1] "IL1RAPL2 MUTATION ANALYSIS"
[1] 3
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 5                 64 
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 5                 64 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
                6                63 
  FAM123B MUTATED FAM123B WILD-TYPE 
                6                63 
[1] "ZIM3 MUTATION ANALYSIS"
[1] 3
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             64 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             64 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "PATHOLOGICSPREAD(PT)"                  
[12] "PATHOLOGICSPREAD(PN)"                  
[13] "PATHOLOGICSPREAD(M)"                   
[14] "TUMORSTAGE"                            
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "COMPLETENESS.OF.RESECTION"             
[17] "NUMBER.OF.LYMPH.NODES"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 69 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
         482          323          412          387          316           NA 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
          NA           NA           NA           31           31           61 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
          NA           NA           31           NA           NA           NA 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 
          30           NA           NA           NA           NA           NA 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
          NA           NA           NA           31           29           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
          NA           NA           NA           28           NA           31 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
          30           30           NA           NA           NA           NA 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
          NA           31           31           NA           31           31 
TCGA-AG-4015 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          NA          637          423          183          789          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
         518          484          396           31          365         2130 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1946          334         1519           NA           NA         1884 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1246         1156         2192 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'PATHOLOGY.T':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGICSPREAD(M)':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "HISTOLOGICAL.TYPE"         "PATHOLOGY.T"              
[5] "PATHOLOGY.N"               "PATHOLOGICSPREAD(M)"      
[7] "TUMOR.STAGE"               "COMPLETENESS.OF.RESECTION"
[9] "NUMBER.OF.LYMPH.NODES"    
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
18 25 16  8 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 69 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGY.T, 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"

$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, 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"

$Table
vv
N0 N1 N2 
43 14 12 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
43 14 12 
PATHOLOGICSPREAD(M), nv=2, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 18  25  16   8 
[1] "table(vv)"
vv
  I  II III  IV 
 18  25  16   8 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 18  25  16   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 18  25  16   8 
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   32  3
  APC WILD-TYPE  6  0
  APC MUTATED APC WILD-TYPE 
           35             6 
  APC MUTATED APC WILD-TYPE 
            3             0 
$`APC MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3583 
       10.62        13.55        12.72        10.39         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.99         1.02         0.95         0.99         0.92 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.94        13.91         6.02        17.03        15.91        13.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       12.00        70.03        63.98        10.98        49.94         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       38.93        61.94        40.96        38.01        72.07 

$`APC WILD-TYPE`
TCGA-AF-2689 TCGA-AG-3582 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A016 
       15.85         1.02         1.02        25.94        23.01         1.02 

  APC MUTATED APC WILD-TYPE 
         0.92          1.02 
  APC MUTATED APC WILD-TYPE 
        72.07         25.94 
  APC MUTATED APC WILD-TYPE 
       10.620         8.435 
[1] "0.9 - 72.1 (10.6)" "1.0 - 25.9 (8.4)" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3587    TCGA-AG-3599 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3726    TCGA-AG-3727    TCGA-AG-3878    TCGA-AG-3887    TCGA-AG-3892 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3893    TCGA-AG-3894    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3587    TCGA-AG-3599 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3726    TCGA-AG-3727    TCGA-AG-3878    TCGA-AG-3887    TCGA-AG-3892 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3893    TCGA-AG-3894    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3587    TCGA-AG-3599 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3726    TCGA-AG-3727    TCGA-AG-3878    TCGA-AG-3887    TCGA-AG-3892 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3893    TCGA-AG-3894    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
[1] "hr="     "8.2e+07"
D1V2, continuous
D1V3, binary
               cls
clus             0  1
  APC MUTATED   25 32
  APC WILD-TYPE  5  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     25   32
  APC WILD-TYPE    5    7
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          25             5
  MALE            32             7
D1V4, binary
               cls
clus             0  1
  APC MUTATED   47  6
  APC WILD-TYPE 10  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     47    6
  APC WILD-TYPE   10    2
                                clus
vv                               APC MUTATED APC WILD-TYPE
  RECTAL ADENOCARCINOMA                   47            10
  RECTAL MUCINOUS ADENOCARCINOMA           6             2
               vv
clus            T1 T2 T3+T4
  APC MUTATED    5 14    38
  APC WILD-TYPE  0  0    12
D1V5, multiclass
       clus
vv      APC MUTATED APC WILD-TYPE
  T1              5             0
  T2             14             0
  T3+T4          38            12
               vv
clus            N0 N1 N2
  APC MUTATED   36 12  9
  APC WILD-TYPE  7  2  3
D1V6, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  N0          36             7
  N1          12             2
  N2           9             3
D1V7, binary
               cls
clus             0  1
  APC MUTATED   50  7
  APC WILD-TYPE  9  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     50    7
  APC WILD-TYPE    9    3
    clus
vv   APC MUTATED APC WILD-TYPE
  M0          50             9
  M1           7             3
               vv
clus             I II III IV
  APC MUTATED   18 18  14  6
  APC WILD-TYPE  0  7   2  2
D1V8, multiclass
     clus
vv    APC MUTATED APC WILD-TYPE
  I            18             0
  II           18             7
  III          14             2
  IV            6             2
               vv
clus            R0 R1 R2
  APC MUTATED   49  1  6
  APC WILD-TYPE 10  0  2
D1V9, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          49            10
  R1           1             0
  R2           6             2
D1V10, continuous

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   25  0
  KRAS WILD-TYPE 13  3
  KRAS MUTATED KRAS WILD-TYPE 
            25             16 
  KRAS MUTATED KRAS WILD-TYPE 
             0              3 
$`KRAS MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3599 
       15.85        10.62        13.55         1.02         2.01         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3999 
        1.02         0.95         0.99         0.92         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
        1.02        13.91         6.02        25.94        23.01        15.91 
TCGA-AG-A015 TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       13.02        70.03        10.98        49.94        61.94        40.96 
TCGA-AG-A032 
       38.01 

$`KRAS WILD-TYPE`
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3893 TCGA-AG-3894 
       12.72        10.39         1.02         1.02         0.99         0.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         1.02        20.94        17.03         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 
       63.98         1.94        38.93        72.07 

  KRAS MUTATED KRAS WILD-TYPE 
          0.92           0.99 
  KRAS MUTATED KRAS WILD-TYPE 
         70.03          72.07 
  KRAS MUTATED KRAS WILD-TYPE 
        10.980          6.165 
[1] "0.9 - 70.0 (11.0)" "1.0 - 72.1 (6.2)" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A036 
"KRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A036 
"KRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A036 
"KRAS WILD-TYPE" 
[1] "hr="     "2.9e+09"
D2V2, continuous
D2V3, 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
D2V4, 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
                vv
clus             T1 T2 T3+T4
  KRAS MUTATED    5  8    25
  KRAS WILD-TYPE  0  6    25
D2V5, multiclass
       clus
vv      KRAS MUTATED KRAS WILD-TYPE
  T1               5              0
  T2               8              6
  T3+T4           25             25
                vv
clus             N0 N1 N2
  KRAS MUTATED   25  7  6
  KRAS WILD-TYPE 18  7  6
D2V6, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  N0           25             18
  N1            7              7
  N2            6              6
D2V7, 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
                vv
clus              I II III IV
  KRAS MUTATED   13 12   9  3
  KRAS WILD-TYPE  5 13   7  5
D2V8, multiclass
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  I             13              5
  II            12             13
  III            9              7
  IV             3              5
                vv
clus             R0 R1 R2
  KRAS MUTATED   36  0  2
  KRAS WILD-TYPE 23  1  6
D2V9, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           36             23
  R1            0              1
  R2            2              6
D2V10, continuous

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   24  2
  TP53 WILD-TYPE 14  1
  TP53 MUTATED TP53 WILD-TYPE 
            26             15 
  TP53 MUTATED TP53 WILD-TYPE 
             2              1 
$`TP53 MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3587 
       15.85        10.62        12.72        10.39         1.02         1.02 
TCGA-AG-3726 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        1.02         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L 
        6.02        23.01        17.03        15.91         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       70.03        63.98        10.98         1.94        61.94        40.96 
TCGA-AG-A032 TCGA-AG-A036 
       38.01        72.07 

$`TP53 WILD-TYPE`
TCGA-AF-2692 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3878 
       13.55         1.02         2.01         0.99         0.95         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H 
        0.92         1.02         0.99        20.94        13.91        25.94 
TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02G 
       13.02        49.94        38.93 

  TP53 MUTATED TP53 WILD-TYPE 
          0.99           0.92 
  TP53 MUTATED TP53 WILD-TYPE 
         72.07          49.94 
  TP53 MUTATED TP53 WILD-TYPE 
         10.80           2.01 
[1] "1.0 - 72.1 (10.8)" "0.9 - 49.9 (2.0)" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A036 
  "TP53 MUTATED" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A036 
  "TP53 MUTATED" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A036 
  "TP53 MUTATED" 
[1] "hr=" "1.1"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  TP53 MUTATED   19 26
  TP53 WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19   26
  TP53 WILD-TYPE   11   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           19             11
  MALE             26             13
D3V4, binary
                cls
clus              0  1
  TP53 MUTATED   41  4
  TP53 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     41    4
  TP53 WILD-TYPE   16    4
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  RECTAL ADENOCARCINOMA                    41             16
  RECTAL MUCINOUS ADENOCARCINOMA            4              4
                vv
clus             T1 T2 T3+T4
  TP53 MUTATED    1  8    36
  TP53 WILD-TYPE  4  6    14
D3V5, multiclass
       clus
vv      TP53 MUTATED TP53 WILD-TYPE
  T1               1              4
  T2               8              6
  T3+T4           36             14
                vv
clus             N0 N1 N2
  TP53 MUTATED   27 10  8
  TP53 WILD-TYPE 16  4  4
D3V6, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  N0           27             16
  N1           10              4
  N2            8              4
D3V7, binary
                cls
clus              0  1
  TP53 MUTATED   39  6
  TP53 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     39    6
  TP53 WILD-TYPE   20    4
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           39             20
  M1            6              4
                vv
clus              I II III IV
  TP53 MUTATED    9 18  12  4
  TP53 WILD-TYPE  9  7   4  4
D3V8, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  I              9              9
  II            18              7
  III           12              4
  IV             4              4
                vv
clus             R0 R1 R2
  TP53 MUTATED   40  1  4
  TP53 WILD-TYPE 19  0  4
D3V9, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           40             19
  R1            1              0
  R2            4              4
D3V10, continuous

Clustering(4) Variable = SMAD4 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED    6  0
  SMAD4 WILD-TYPE 32  3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              6              35 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              0               3 
$`SMAD4 MUTATED`
TCGA-AG-3887 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A02X 
        0.92        13.91        17.03         1.02        10.98        40.96 

$`SMAD4 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.99         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        20.94         6.02        25.94        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 
       15.91        13.02        12.00        70.03        63.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.93        61.94        38.01        72.07 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.92            0.95 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          40.96           72.07 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
         12.445          10.390 
[1] "0.9 - 41.0 (12.4)" "0.9 - 72.1 (10.4)"
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD4 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD4 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD4 WILD-TYPE" 
[1] "hr="     "2.4e+08"
D4V2, continuous
D4V3, 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
D4V4, 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
                 vv
clus              T1 T2 T3+T4
  SMAD4 MUTATED    0  2     6
  SMAD4 WILD-TYPE  5 12    44
D4V5, multiclass
       clus
vv      SMAD4 MUTATED SMAD4 WILD-TYPE
  T1                0               5
  T2                2              12
  T3+T4             6              44
                 vv
clus              N0 N1 N2
  SMAD4 MUTATED    4  2  2
  SMAD4 WILD-TYPE 39 12 10
D4V6, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  N0             4              39
  N1             2              12
  N2             2              10
D4V7, 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
                 vv
clus               I II III IV
  SMAD4 MUTATED    2  2   2  2
  SMAD4 WILD-TYPE 16 23  14  6
D4V8, multiclass
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  I               2              16
  II              2              23
  III             2              14
  IV              2               6
                 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
D4V10, continuous

Clustering(5) Variable = KIAA1804 MUTATION ANALYSIS
D5V1, survival
                    sevent
clus2                 0  1
  KIAA1804 MUTATED    6  0
  KIAA1804 WILD-TYPE 32  3
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 6                 35 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
                 0                  3 
$`KIAA1804 MUTATED`
TCGA-AF-2691 TCGA-AG-3582 TCGA-AG-3727 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A02N 
       10.62         1.02         0.95        20.94        13.91        61.94 

$`KIAA1804 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3583 
       15.85        13.55        12.72        10.39         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         1.02         0.99         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
        0.99         0.99         1.02         1.02         1.02         1.02 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.94        23.01        17.03        15.91        13.02 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        1.02        12.00        70.03        63.98        10.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.93        40.96        38.01        72.07 

  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
              0.95               0.92 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
             61.94              72.07 
  KIAA1804 MUTATED KIAA1804 WILD-TYPE 
            12.265             10.390 
[1] "0.9 - 61.9 (12.3)" "0.9 - 72.1 (10.4)"
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "KIAA1804 MUTATED"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "KIAA1804 MUTATED"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
  "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "KIAA1804 MUTATED"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"KIAA1804 WILD-TYPE"   "KIAA1804 MUTATED" "KIAA1804 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"KIAA1804 WILD-TYPE" "KIAA1804 WILD-TYPE" 
[1] "hr="     "2.4e+08"
D5V2, continuous
D5V3, 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
D5V4, 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
                    vv
clus                 T1 T2 T3+T4
  KIAA1804 MUTATED    1  2     6
  KIAA1804 WILD-TYPE  4 12    44
D5V5, multiclass
       clus
vv      KIAA1804 MUTATED KIAA1804 WILD-TYPE
  T1                   1                  4
  T2                   2                 12
  T3+T4                6                 44
                    vv
clus                 N0 N1 N2
  KIAA1804 MUTATED    6  2  1
  KIAA1804 WILD-TYPE 37 12 11
D5V6, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  N0                6                 37
  N1                2                 12
  N2                1                 11
D5V7, 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
                    vv
clus                  I II III IV
  KIAA1804 MUTATED    3  3   2  1
  KIAA1804 WILD-TYPE 15 22  14  7
D5V8, multiclass
     clus
vv    KIAA1804 MUTATED KIAA1804 WILD-TYPE
  I                  3                 15
  II                 3                 22
  III                2                 14
  IV                 1                  7
                    vv
clus                 R0 R1 R2
  KIAA1804 MUTATED    8  0  1
  KIAA1804 WILD-TYPE 51  1  7
D5V9, multiclass
    clus
vv   KIAA1804 MUTATED KIAA1804 WILD-TYPE
  R0                8                 51
  R1                0                  1
  R2                1                  7
D5V10, continuous

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED    4  0
  FBXW7 WILD-TYPE 34  3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              4              37 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              0               3 
$`FBXW7 MUTATED`
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A02N 
        1.02        20.94        17.03        61.94 

$`FBXW7 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.99         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        13.91         6.02        25.94        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.91        13.02         1.02        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.94         1.94        38.93        40.96        38.01 
TCGA-AG-A036 
       72.07 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           1.02            0.92 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          61.94           72.07 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
         18.985          10.390 
[1] "1.0 - 61.9 (19.0)" "0.9 - 72.1 (10.4)"
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A036 
"FBXW7 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A036 
"FBXW7 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AG-A036 
"FBXW7 WILD-TYPE" 
[1] "hr="     "2.2e+08"
D6V2, continuous
D6V3, 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
D6V4, 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
                 vv
clus              T1 T2 T3+T4
  FBXW7 MUTATED    1  1     7
  FBXW7 WILD-TYPE  4 13    43
D6V5, multiclass
       clus
vv      FBXW7 MUTATED FBXW7 WILD-TYPE
  T1                1               4
  T2                1              13
  T3+T4             7              43
                 vv
clus              N0 N1 N2
  FBXW7 MUTATED    8  0  1
  FBXW7 WILD-TYPE 35 14 11
D6V6, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  N0             8              35
  N1             0              14
  N2             1              11
D6V7, 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
                 vv
clus               I II III IV
  FBXW7 MUTATED    2  6   1  0
  FBXW7 WILD-TYPE 16 19  15  8
D6V8, multiclass
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  I               2              16
  II              6              19
  III             1              15
  IV              0               8
                 vv
clus              R0 R1 R2
  FBXW7 MUTATED    8  0  0
  FBXW7 WILD-TYPE 51  1  8
D6V9, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0             8              51
  R1             0               1
  R2             0               8
D6V10, continuous

Clustering(7) Variable = NRAS MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  NRAS MUTATED    4  1
  NRAS WILD-TYPE 34  2
  NRAS MUTATED NRAS WILD-TYPE 
             5             36 
  NRAS MUTATED NRAS WILD-TYPE 
             1              2 
$`NRAS MUTATED`
TCGA-AF-2691 TCGA-AF-3913 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A01L 
       10.62        10.39         1.02         0.99        12.00 

$`NRAS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       15.85        13.55        12.72         1.02         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 
        1.02         0.99         1.02         0.95         0.99         0.92 
TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
        0.99         1.02         1.02         1.02         1.02        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
       13.02         1.02        70.03        63.98        10.98        49.94 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        38.93        61.94        40.96        38.01        72.07 

  NRAS MUTATED NRAS WILD-TYPE 
          0.99           0.92 
  NRAS MUTATED NRAS WILD-TYPE 
         12.00          72.07 
  NRAS MUTATED NRAS WILD-TYPE 
         10.39          11.85 
[1] "1.0 - 12.0 (10.4)" "0.9 - 72.1 (11.9)"
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A036 
"NRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A036 
"NRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
  "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AG-A036 
"NRAS WILD-TYPE" 
[1] "hr=" "6.8"
D7V2, continuous
D7V3, 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
D7V4, 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
                vv
clus             T1 T2 T3+T4
  NRAS MUTATED    2  0     3
  NRAS WILD-TYPE  3 14    47
D7V5, multiclass
       clus
vv      NRAS MUTATED NRAS WILD-TYPE
  T1               2              3
  T2               0             14
  T3+T4            3             47
                vv
clus             N0 N1 N2
  NRAS MUTATED    3  2  0
  NRAS WILD-TYPE 40 12 12
D7V6, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  N0            3             40
  N1            2             12
  N2            0             12
D7V7, 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
                vv
clus              I II III IV
  NRAS MUTATED    2  1   1  0
  NRAS WILD-TYPE 16 24  15  8
D7V8, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  I              2             16
  II             1             24
  III            1             15
  IV             0              8
                vv
clus             R0 R1 R2
  NRAS MUTATED    5  0  0
  NRAS WILD-TYPE 54  1  8
D7V9, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0            5             54
  R1            0              1
  R2            0              8
D7V10, continuous

Clustering(8) Variable = TCF7L2 MUTATION ANALYSIS
D8V1, survival
                  sevent
clus2               0  1
  TCF7L2 MUTATED    5  0
  TCF7L2 WILD-TYPE 33  3
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               5               36 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
               0                3 
$`TCF7L2 MUTATED`
TCGA-AF-2692 TCGA-AG-3582 TCGA-AG-3726 TCGA-AG-4007 TCGA-AG-A032 
       13.55         1.02         1.02         1.02        38.01 

$`TCF7L2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3583 
       15.85        10.62        12.72        10.39         1.02         2.01 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
        1.02         0.99         0.95         0.99         0.92         1.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 
        0.99         0.99         1.02         1.02         1.02        20.94 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.91         6.02        25.94        23.01        17.03        15.91 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       13.02         1.02        12.00        70.03        63.98        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A036 
       49.94         1.94        38.93        61.94        40.96        72.07 

  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            1.02             0.92 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
           38.01            72.07 
  TCF7L2 MUTATED TCF7L2 WILD-TYPE 
            1.02            10.80 
[1] "1.0 - 38.0 (1.0)"  "0.9 - 72.1 (10.8)"
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-A036 
"TCF7L2 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-A036 
"TCF7L2 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE" "TCF7L2 WILD-TYPE"   "TCF7L2 MUTATED" 
      TCGA-AG-A036 
"TCF7L2 WILD-TYPE" 
[1] "hr="     "7.6e+07"
D8V2, continuous
D8V3, 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
D8V4, 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
                  vv
clus               T1 T2 T3+T4
  TCF7L2 MUTATED    0  2     5
  TCF7L2 WILD-TYPE  5 12    45
D8V5, multiclass
       clus
vv      TCF7L2 MUTATED TCF7L2 WILD-TYPE
  T1                 0                5
  T2                 2               12
  T3+T4              5               45
                  vv
clus               N0 N1 N2
  TCF7L2 MUTATED    4  2  1
  TCF7L2 WILD-TYPE 39 12 11
D8V6, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  N0              4               39
  N1              2               12
  N2              1               11
D8V7, 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
                  vv
clus                I II III IV
  TCF7L2 MUTATED    2  2   1  2
  TCF7L2 WILD-TYPE 16 23  15  6
D8V8, multiclass
     clus
vv    TCF7L2 MUTATED TCF7L2 WILD-TYPE
  I                2               16
  II               2               23
  III              1               15
  IV               2                6
                  vv
clus               R0 R1 R2
  TCF7L2 MUTATED    5  0  2
  TCF7L2 WILD-TYPE 54  1  6
D8V9, multiclass
    clus
vv   TCF7L2 MUTATED TCF7L2 WILD-TYPE
  R0              5               54
  R1              0                1
  R2              2                6
D8V10, continuous

Clustering(9) Variable = PIK3CA MUTATION ANALYSIS
D9V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED    5  0
  PIK3CA WILD-TYPE 33  3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5               36 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               0                3 
$`PIK3CA MUTATED`
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-A00H TCGA-AG-A020 TCGA-AG-A02N 
        0.99         0.92        25.94        10.98        61.94 

$`PIK3CA WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        1.02         0.99         0.99         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.94        13.91         6.02        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.91        13.02         1.02        12.00        70.03        63.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.94         1.94        38.93        40.96        38.01        72.07 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.92             0.95 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           61.94            72.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
          10.980           10.505 
[1] "0.9 - 61.9 (11.0)" "0.9 - 72.1 (10.5)"
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A036 
"PIK3CA WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A036 
"PIK3CA WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AG-A036 
"PIK3CA WILD-TYPE" 
[1] "hr="     "2.2e+08"
D9V2, continuous
D9V3, binary
                  cls
clus                0  1
  PIK3CA MUTATED    3  4
  PIK3CA WILD-TYPE 27 35
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3    4
  PIK3CA WILD-TYPE   27   35
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              3               27
  MALE                4               35
D9V4, binary
                  cls
clus                0  1
  PIK3CA MUTATED    4  3
  PIK3CA WILD-TYPE 53  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      4    3
  PIK3CA WILD-TYPE   53    5
                                clus
vv                               PIK3CA MUTATED PIK3CA WILD-TYPE
  RECTAL ADENOCARCINOMA                       4               53
  RECTAL MUCINOUS ADENOCARCINOMA              3                5
                  vv
clus               T1 T2 T3+T4
  PIK3CA MUTATED    0  1     6
  PIK3CA WILD-TYPE  5 13    44
D9V5, multiclass
       clus
vv      PIK3CA MUTATED PIK3CA WILD-TYPE
  T1                 0                5
  T2                 1               13
  T3+T4              6               44
                  vv
clus               N0 N1 N2
  PIK3CA MUTATED    5  2  0
  PIK3CA WILD-TYPE 38 12 12
D9V6, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0              5               38
  N1              2               12
  N2              0               12
D9V7, binary
                  cls
clus                0  1
  PIK3CA MUTATED    7  0
  PIK3CA WILD-TYPE 52 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      7    0
  PIK3CA WILD-TYPE   52   10
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              7               52
  M1              0               10
                  vv
clus                I II III IV
  PIK3CA MUTATED    1  4   2  0
  PIK3CA WILD-TYPE 17 21  14  8
D9V8, multiclass
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  I                1               17
  II               4               21
  III              2               14
  IV               0                8
                  vv
clus               R0 R1 R2
  PIK3CA MUTATED    7  0  0
  PIK3CA WILD-TYPE 52  1  8
D9V9, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0              7               52
  R1              0                1
  R2              0                8
D9V10, continuous

Clustering(10) Variable = OPCML MUTATION ANALYSIS
D10V1, survival
                 sevent
clus2              0  1
  OPCML MUTATED    4  0
  OPCML WILD-TYPE 34  3
  OPCML MUTATED OPCML WILD-TYPE 
              4              37 
  OPCML MUTATED OPCML WILD-TYPE 
              0               3 
$`OPCML MUTATED`
TCGA-AG-3726 TCGA-AG-A002 TCGA-AG-A02X TCGA-AG-A032 
        1.02        20.94        40.96        38.01 

$`OPCML WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3727 TCGA-AG-3878 
        1.02         2.01         1.02         0.99         0.95         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       17.03        15.91        13.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        10.98        49.94         1.94        38.93        61.94 
TCGA-AG-A036 
       72.07 

  OPCML MUTATED OPCML WILD-TYPE 
           1.02            0.92 
  OPCML MUTATED OPCML WILD-TYPE 
          40.96           72.07 
  OPCML MUTATED OPCML WILD-TYPE 
         29.475          10.390 
[1] "1.0 - 41.0 (29.5)" "0.9 - 72.1 (10.4)"
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED"   "OPCML MUTATED" 
     TCGA-AG-A036 
"OPCML WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED"   "OPCML MUTATED" 
     TCGA-AG-A036 
"OPCML WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"OPCML WILD-TYPE"   "OPCML MUTATED" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" "OPCML WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"OPCML WILD-TYPE" "OPCML WILD-TYPE"   "OPCML MUTATED"   "OPCML MUTATED" 
     TCGA-AG-A036 
"OPCML WILD-TYPE" 
[1] "hr="     "2.2e+08"
D10V2, continuous
D10V3, binary
                 cls
clus               0  1
  OPCML MUTATED    2  4
  OPCML WILD-TYPE 28 35
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPCML MUTATED      2    4
  OPCML WILD-TYPE   28   35
        clus
vv       OPCML MUTATED OPCML WILD-TYPE
  FEMALE             2              28
  MALE               4              35
D10V4, binary
                 cls
clus               0  1
  OPCML MUTATED    6  0
  OPCML WILD-TYPE 51  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPCML MUTATED      6    0
  OPCML WILD-TYPE   51    8
                                clus
vv                               OPCML MUTATED OPCML WILD-TYPE
  RECTAL ADENOCARCINOMA                      6              51
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
                 vv
clus              T1 T2 T3+T4
  OPCML MUTATED    0  3     3
  OPCML WILD-TYPE  5 11    47
D10V5, multiclass
       clus
vv      OPCML MUTATED OPCML WILD-TYPE
  T1                0               5
  T2                3              11
  T3+T4             3              47
                 vv
clus              N0 N1 N2
  OPCML MUTATED    4  1  1
  OPCML WILD-TYPE 39 13 11
D10V6, multiclass
    clus
vv   OPCML MUTATED OPCML WILD-TYPE
  N0             4              39
  N1             1              13
  N2             1              11
D10V7, binary
                 cls
clus               0  1
  OPCML MUTATED    5  1
  OPCML WILD-TYPE 54  9
[1] "tbl2"
                 cls
clus              [,1] [,2]
  OPCML MUTATED      5    1
  OPCML WILD-TYPE   54    9
    clus
vv   OPCML MUTATED OPCML WILD-TYPE
  M0             5              54
  M1             1               9
                 vv
clus               I II III IV
  OPCML MUTATED    3  1   1  1
  OPCML WILD-TYPE 15 24  15  7
D10V8, multiclass
     clus
vv    OPCML MUTATED OPCML WILD-TYPE
  I               3              15
  II              1              24
  III             1              15
  IV              1               7
                 vv
clus              R0 R1 R2
  OPCML MUTATED    6  0  0
  OPCML WILD-TYPE 53  1  8
D10V9, multiclass
    clus
vv   OPCML MUTATED OPCML WILD-TYPE
  R0             6              53
  R1             0               1
  R2             0               8
D10V10, continuous

Clustering(11) Variable = SMAD2 MUTATION ANALYSIS
D11V1, survival
                 sevent
clus2              0  1
  SMAD2 MUTATED    3  0
  SMAD2 WILD-TYPE 35  3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              3              38 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              0               3 
$`SMAD2 MUTATED`
TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A01W 
       20.94        17.03        70.03 

$`SMAD2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02         1.02        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01Y 
       23.01        15.91        13.02         1.02        12.00        63.98 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AG-A036 
       38.01        72.07 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
          17.03            0.92 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          70.03           72.07 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
         20.940           8.205 
[1] "17.0 - 70.0 (20.9)" "0.9 - 72.1 (8.2)"  
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD2 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD2 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AG-A036 
"SMAD2 WILD-TYPE" 
[1] "hr="     "2.2e+08"
D11V2, continuous
D11V3, binary
                 cls
clus               0  1
  SMAD2 MUTATED    2  3
  SMAD2 WILD-TYPE 28 36
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      2    3
  SMAD2 WILD-TYPE   28   36
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             2              28
  MALE               3              36
D11V4, binary
                 cls
clus               0  1
  SMAD2 MUTATED    5  0
  SMAD2 WILD-TYPE 52  8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      5    0
  SMAD2 WILD-TYPE   52    8
                                clus
vv                               SMAD2 MUTATED SMAD2 WILD-TYPE
  RECTAL ADENOCARCINOMA                      5              52
  RECTAL MUCINOUS ADENOCARCINOMA             0               8
                 vv
clus              T1 T2 T3+T4
  SMAD2 MUTATED    0  2     3
  SMAD2 WILD-TYPE  5 12    47
D11V5, multiclass
       clus
vv      SMAD2 MUTATED SMAD2 WILD-TYPE
  T1                0               5
  T2                2              12
  T3+T4             3              47
                 vv
clus              N0 N1 N2
  SMAD2 MUTATED    5  0  0
  SMAD2 WILD-TYPE 38 14 12
D11V6, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  N0             5              38
  N1             0              14
  N2             0              12
D11V7, binary
                 cls
clus               0  1
  SMAD2 MUTATED    5  0
  SMAD2 WILD-TYPE 54 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      5    0
  SMAD2 WILD-TYPE   54   10
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  M0             5              54
  M1             0              10
                 vv
clus               I II III IV
  SMAD2 MUTATED    2  3   0  0
  SMAD2 WILD-TYPE 16 22  16  8
D11V8, multiclass
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  I               2              16
  II              3              22
  III             0              16
  IV              0               8
                 vv
clus              R0 R1 R2
  SMAD2 MUTATED    5  0  0
  SMAD2 WILD-TYPE 54  1  8
D11V9, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             5              54
  R1             0               1
  R2             0               8
D11V10, continuous

Clustering(12) Variable = SPATA8 MUTATION ANALYSIS
D12V1, survival
                  sevent
clus2               0  1
  SPATA8 MUTATED    2  0
  SPATA8 WILD-TYPE 36  3
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               39 
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               0                3 
$`SPATA8 MUTATED`
TCGA-AG-4001 TCGA-AG-A01W 
        1.02        70.03 

$`SPATA8 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 
        0.99         0.92         1.02         0.99         0.99         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         1.02        20.94        13.91         6.02        25.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        17.03        15.91        13.02         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        10.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       40.96        38.01        72.07 

  SPATA8 MUTATED SPATA8 WILD-TYPE 
            1.02             0.92 
  SPATA8 MUTATED SPATA8 WILD-TYPE 
           70.03            72.07 
  SPATA8 MUTATED SPATA8 WILD-TYPE 
          35.525           10.620 
[1] "1.0 - 70.0 (35.5)" "0.9 - 72.1 (10.6)"
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" "SPATA8 WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A036 
"SPATA8 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" "SPATA8 WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A036 
"SPATA8 WILD-TYPE" 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4001       TCGA-AG-4007 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" "SPATA8 WILD-TYPE" 
      TCGA-AG-4008       TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A00H       TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A015       TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01W 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE"   "SPATA8 MUTATED" 
      TCGA-AG-A01Y       TCGA-AG-A020       TCGA-AG-A025       TCGA-AG-A026 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02G       TCGA-AG-A02N       TCGA-AG-A02X       TCGA-AG-A032 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A036 
"SPATA8 WILD-TYPE" 
[1] "Remove cluster labels:" "SPATA8 MUTATED"        
clus
  SPATA8 MUTATED SPATA8 WILD-TYPE 
               2               39 
      TCGA-AF-2689       TCGA-AF-2691       TCGA-AF-2692       TCGA-AF-3400 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AF-3913       TCGA-AG-3581       TCGA-AG-3582       TCGA-AG-3583 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3587       TCGA-AG-3599       TCGA-AG-3726       TCGA-AG-3727 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3878       TCGA-AG-3887       TCGA-AG-3892       TCGA-AG-3893 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-3894       TCGA-AG-3999       TCGA-AG-4007       TCGA-AG-4008 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A002       TCGA-AG-A008       TCGA-AG-A00C       TCGA-AG-A00H 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A00Y       TCGA-AG-A011       TCGA-AG-A014       TCGA-AG-A015 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A016       TCGA-AG-A01L       TCGA-AG-A01Y       TCGA-AG-A020 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A025       TCGA-AG-A026       TCGA-AG-A02G       TCGA-AG-A02N 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
      TCGA-AG-A02X       TCGA-AG-A032       TCGA-AG-A036 
"SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" "SPATA8 WILD-TYPE" 
D12V2, continuous
D12V3, binary
                  cls
clus                0  1
  SPATA8 MUTATED    3  0
  SPATA8 WILD-TYPE 27 39
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA8 MUTATED      3    0
  SPATA8 WILD-TYPE   27   39
        clus
vv       SPATA8 MUTATED SPATA8 WILD-TYPE
  FEMALE              3               27
  MALE                0               39
D12V4, binary
                  cls
clus                0  1
  SPATA8 MUTATED    3  0
  SPATA8 WILD-TYPE 54  8
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA8 MUTATED      3    0
  SPATA8 WILD-TYPE   54    8
                                clus
vv                               SPATA8 MUTATED SPATA8 WILD-TYPE
  RECTAL ADENOCARCINOMA                       3               54
  RECTAL MUCINOUS ADENOCARCINOMA              0                8
                  vv
clus               T1 T2 T3+T4
  SPATA8 MUTATED    0  0     3
  SPATA8 WILD-TYPE  5 14    47
D12V5, multiclass
       clus
vv      SPATA8 MUTATED SPATA8 WILD-TYPE
  T1                 0                5
  T2                 0               14
  T3+T4              3               47
                  vv
clus               N0 N1 N2
  SPATA8 MUTATED    2  1  0
  SPATA8 WILD-TYPE 41 13 12
D12V6, multiclass
    clus
vv   SPATA8 MUTATED SPATA8 WILD-TYPE
  N0              2               41
  N1              1               13
  N2              0               12
D12V7, binary
                  cls
clus                0  1
  SPATA8 MUTATED    3  0
  SPATA8 WILD-TYPE 56 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  SPATA8 MUTATED      3    0
  SPATA8 WILD-TYPE   56   10
    clus
vv   SPATA8 MUTATED SPATA8 WILD-TYPE
  M0              3               56
  M1              0               10
                  vv
clus                I II III IV
  SPATA8 MUTATED    0  2   1  0
  SPATA8 WILD-TYPE 18 23  15  8
D12V8, multiclass
     clus
vv    SPATA8 MUTATED SPATA8 WILD-TYPE
  I                0               18
  II               2               23
  III              1               15
  IV               0                8
                  vv
clus               R0 R1 R2
  SPATA8 MUTATED    3  0  0
  SPATA8 WILD-TYPE 56  1  8
D12V9, multiclass
    clus
vv   SPATA8 MUTATED SPATA8 WILD-TYPE
  R0              3               56
  R1              0                1
  R2              0                8
D12V10, continuous

Clustering(13) Variable = ERBB2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  ERBB2 MUTATED    2  0
  ERBB2 WILD-TYPE 36  3
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              2              39 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              0               3 
$`ERBB2 MUTATED`
TCGA-AG-3599 TCGA-AG-A002 
        0.99        20.94 

$`ERBB2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        1.02         2.01         1.02         1.02         0.95         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.92         1.02         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       17.03        15.91        13.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        10.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       40.96        38.01        72.07 

  ERBB2 MUTATED ERBB2 WILD-TYPE 
           0.99            0.92 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
          20.94           72.07 
  ERBB2 MUTATED ERBB2 WILD-TYPE 
         10.965          10.620 
[1] "1.0 - 20.9 (11.0)" "0.9 - 72.1 (10.6)"
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A036 
"ERBB2 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A036 
"ERBB2 WILD-TYPE" 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3599      TCGA-AG-3726      TCGA-AG-3727 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3878      TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3894      TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-4008      TCGA-AG-A002      TCGA-AG-A008      TCGA-AG-A00C 
"ERBB2 WILD-TYPE"   "ERBB2 MUTATED" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A00H      TCGA-AG-A00Y      TCGA-AG-A011      TCGA-AG-A014 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A015      TCGA-AG-A016      TCGA-AG-A01L      TCGA-AG-A01W 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A01Y      TCGA-AG-A020      TCGA-AG-A025      TCGA-AG-A026 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A02G      TCGA-AG-A02N      TCGA-AG-A02X      TCGA-AG-A032 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A036 
"ERBB2 WILD-TYPE" 
[1] "Remove cluster labels:" "ERBB2 MUTATED"         
clus
  ERBB2 MUTATED ERBB2 WILD-TYPE 
              2              39 
     TCGA-AF-2689      TCGA-AF-2691      TCGA-AF-2692      TCGA-AF-3400 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AF-3913      TCGA-AG-3581      TCGA-AG-3582      TCGA-AG-3583 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3587      TCGA-AG-3726      TCGA-AG-3727      TCGA-AG-3878 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3887      TCGA-AG-3892      TCGA-AG-3893      TCGA-AG-3894 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-3999      TCGA-AG-4001      TCGA-AG-4007      TCGA-AG-4008 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A008      TCGA-AG-A00C      TCGA-AG-A00H      TCGA-AG-A00Y 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A011      TCGA-AG-A014      TCGA-AG-A015      TCGA-AG-A016 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A01L      TCGA-AG-A01W      TCGA-AG-A01Y      TCGA-AG-A020 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A025      TCGA-AG-A026      TCGA-AG-A02G      TCGA-AG-A02N 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
     TCGA-AG-A02X      TCGA-AG-A032      TCGA-AG-A036 
"ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" "ERBB2 WILD-TYPE" 
D13V2, continuous
D13V3, 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
D13V4, 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
                 vv
clus              T1 T2 T3+T4
  ERBB2 MUTATED    0  2     2
  ERBB2 WILD-TYPE  5 12    48
D13V5, multiclass
       clus
vv      ERBB2 MUTATED ERBB2 WILD-TYPE
  T1                0               5
  T2                2              12
  T3+T4             2              48
                 vv
clus              N0 N1 N2
  ERBB2 MUTATED    4  0  0
  ERBB2 WILD-TYPE 39 14 12
D13V6, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  N0             4              39
  N1             0              14
  N2             0              12
D13V7, 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
                 vv
clus               I II III IV
  ERBB2 MUTATED    2  2   0  0
  ERBB2 WILD-TYPE 16 23  16  8
D13V8, multiclass
     clus
vv    ERBB2 MUTATED ERBB2 WILD-TYPE
  I               2              16
  II              2              23
  III             0              16
  IV              0               8
                 vv
clus              R0 R1 R2
  ERBB2 MUTATED    4  0  0
  ERBB2 WILD-TYPE 55  1  8
D13V9, multiclass
    clus
vv   ERBB2 MUTATED ERBB2 WILD-TYPE
  R0             4              55
  R1             0               1
  R2             0               8
D13V10, continuous

Clustering(14) Variable = IL1RAPL2 MUTATION ANALYSIS
D14V1, survival
                    sevent
clus2                 0  1
  IL1RAPL2 MUTATED    3  0
  IL1RAPL2 WILD-TYPE 35  3
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 3                 38 
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
                 0                  3 
$`IL1RAPL2 MUTATED`
TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-A002 
        0.92         0.99        20.94 

$`IL1RAPL2 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         1.02         0.99         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.91        13.02         1.02        12.00        70.03        63.98 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.94         1.94        38.93        61.94        40.96 
TCGA-AG-A032 TCGA-AG-A036 
       38.01        72.07 

  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
              0.92               0.95 
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
             20.94              72.07 
  IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE 
              0.99              10.80 
[1] "0.9 - 20.9 (1.0)"  "0.9 - 72.1 (10.8)"
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AF-2689         TCGA-AF-2691         TCGA-AF-2692 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3913         TCGA-AG-3581 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3582         TCGA-AG-3583         TCGA-AG-3587 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3599         TCGA-AG-3726         TCGA-AG-3727 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3878         TCGA-AG-3887         TCGA-AG-3892 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-3893         TCGA-AG-3894         TCGA-AG-3999 
"IL1RAPL2 WILD-TYPE"   "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-4001         TCGA-AG-4007         TCGA-AG-4008 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A002         TCGA-AG-A008         TCGA-AG-A00C 
  "IL1RAPL2 MUTATED" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A00H         TCGA-AG-A00Y         TCGA-AG-A011 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A014         TCGA-AG-A015         TCGA-AG-A016 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A01L         TCGA-AG-A01W         TCGA-AG-A01Y 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A020         TCGA-AG-A025         TCGA-AG-A026 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A02G         TCGA-AG-A02N         TCGA-AG-A02X 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
        TCGA-AG-A032         TCGA-AG-A036 
"IL1RAPL2 WILD-TYPE" "IL1RAPL2 WILD-TYPE" 
[1] "hr="     "2.6e+07"
D14V2, continuous
D14V3, binary
                    cls
clus                  0  1
  IL1RAPL2 MUTATED    2  3
  IL1RAPL2 WILD-TYPE 28 36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL2 MUTATED      2    3
  IL1RAPL2 WILD-TYPE   28   36
        clus
vv       IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  FEMALE                2                 28
  MALE                  3                 36
D14V4, binary
                    cls
clus                  0  1
  IL1RAPL2 MUTATED    3  2
  IL1RAPL2 WILD-TYPE 54  6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL2 MUTATED      3    2
  IL1RAPL2 WILD-TYPE   54    6
                                clus
vv                               IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  RECTAL ADENOCARCINOMA                         3                 54
  RECTAL MUCINOUS ADENOCARCINOMA                2                  6
                    vv
clus                 T1 T2 T3+T4
  IL1RAPL2 MUTATED    0  1     4
  IL1RAPL2 WILD-TYPE  5 13    46
D14V5, multiclass
       clus
vv      IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  T1                   0                  5
  T2                   1                 13
  T3+T4                4                 46
                    vv
clus                 N0 N1 N2
  IL1RAPL2 MUTATED    4  1  0
  IL1RAPL2 WILD-TYPE 39 13 12
D14V6, multiclass
    clus
vv   IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  N0                4                 39
  N1                1                 13
  N2                0                 12
D14V7, binary
                    cls
clus                  0  1
  IL1RAPL2 MUTATED    5  0
  IL1RAPL2 WILD-TYPE 54 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  IL1RAPL2 MUTATED      5    0
  IL1RAPL2 WILD-TYPE   54   10
    clus
vv   IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  M0                5                 54
  M1                0                 10
                    vv
clus                  I II III IV
  IL1RAPL2 MUTATED    1  3   1  0
  IL1RAPL2 WILD-TYPE 17 22  15  8
D14V8, multiclass
     clus
vv    IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  I                  1                 17
  II                 3                 22
  III                1                 15
  IV                 0                  8
                    vv
clus                 R0 R1 R2
  IL1RAPL2 MUTATED    5  0  0
  IL1RAPL2 WILD-TYPE 54  1  8
D14V9, multiclass
    clus
vv   IL1RAPL2 MUTATED IL1RAPL2 WILD-TYPE
  R0                5                 54
  R1                0                  1
  R2                0                  8
D14V10, continuous

Clustering(15) Variable = FAM123B MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  FAM123B MUTATED    3  1
  FAM123B WILD-TYPE 35  2
  FAM123B MUTATED FAM123B WILD-TYPE 
                4                37 
  FAM123B MUTATED FAM123B WILD-TYPE 
                1                 2 
$`FAM123B MUTATED`
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A02G TCGA-AG-A02N 
        1.02        20.94        38.93        61.94 

$`FAM123B WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 
        0.99         0.92         0.99         0.99         1.02         1.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        13.91         6.02        25.94        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
       17.03        15.91        13.02         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       63.98        10.98        49.94         1.94        40.96        38.01 
TCGA-AG-A036 
       72.07 

  FAM123B MUTATED FAM123B WILD-TYPE 
             1.02              0.92 
  FAM123B MUTATED FAM123B WILD-TYPE 
            61.94             72.07 
  FAM123B MUTATED FAM123B WILD-TYPE 
           29.935            10.390 
[1] "1.0 - 61.9 (29.9)" "0.9 - 72.1 (10.4)"
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726        TCGA-AG-3727 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "FAM123B MUTATED"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A036 
"FAM123B WILD-TYPE" 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726        TCGA-AG-3727 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "FAM123B MUTATED"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A036 
"FAM123B WILD-TYPE" 
       TCGA-AF-2689        TCGA-AF-2691        TCGA-AF-2692        TCGA-AF-3400 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AF-3913        TCGA-AG-3581        TCGA-AG-3582        TCGA-AG-3583 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3587        TCGA-AG-3599        TCGA-AG-3726        TCGA-AG-3727 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-3878        TCGA-AG-3887        TCGA-AG-3892        TCGA-AG-3893 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AG-3894        TCGA-AG-3999        TCGA-AG-4001        TCGA-AG-4007 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-4008        TCGA-AG-A002        TCGA-AG-A008        TCGA-AG-A00C 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A00H        TCGA-AG-A00Y        TCGA-AG-A011        TCGA-AG-A014 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A015        TCGA-AG-A016        TCGA-AG-A01L        TCGA-AG-A01W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A01Y        TCGA-AG-A020        TCGA-AG-A025        TCGA-AG-A026 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A02G        TCGA-AG-A02N        TCGA-AG-A02X        TCGA-AG-A032 
  "FAM123B MUTATED"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AG-A036 
"FAM123B WILD-TYPE" 
[1] "hr=" "2.4"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  FAM123B MUTATED    2  4
  FAM123B WILD-TYPE 28 35
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      2    4
  FAM123B WILD-TYPE   28   35
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE               2                28
  MALE                 4                35
D15V4, binary
                   cls
clus                 0  1
  FAM123B MUTATED    6  0
  FAM123B WILD-TYPE 51  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      6    0
  FAM123B WILD-TYPE   51    8
                                clus
vv                               FAM123B MUTATED FAM123B WILD-TYPE
  RECTAL ADENOCARCINOMA                        6                51
  RECTAL MUCINOUS ADENOCARCINOMA               0                 8
                   vv
clus                T1 T2 T3+T4
  FAM123B MUTATED    1  3     2
  FAM123B WILD-TYPE  4 11    48
D15V5, multiclass
       clus
vv      FAM123B MUTATED FAM123B WILD-TYPE
  T1                  1                 4
  T2                  3                11
  T3+T4               2                48
                   vv
clus                N0 N1 N2
  FAM123B MUTATED    4  1  1
  FAM123B WILD-TYPE 39 13 11
D15V6, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  N0               4                39
  N1               1                13
  N2               1                11
D15V7, binary
                   cls
clus                 0  1
  FAM123B MUTATED    4  2
  FAM123B WILD-TYPE 55  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED      4    2
  FAM123B WILD-TYPE   55    8
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  M0               4                55
  M1               2                 8
                   vv
clus                 I II III IV
  FAM123B MUTATED    3  1   0  2
  FAM123B WILD-TYPE 15 24  16  6
D15V8, multiclass
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  I                 3                15
  II                1                24
  III               0                16
  IV                2                 6
                   vv
clus                R0 R1 R2
  FAM123B MUTATED    4  0  2
  FAM123B WILD-TYPE 55  1  6
D15V9, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0               4                55
  R1               0                 1
  R2               2                 6
D15V10, continuous

Clustering(16) Variable = ZIM3 MUTATION ANALYSIS
D16V1, survival
                sevent
clus2             0  1
  ZIM3 MUTATED    4  1
  ZIM3 WILD-TYPE 34  2
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             5             36 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
             1              2 
$`ZIM3 MUTATED`
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-A002 TCGA-AG-A020 TCGA-AG-A026 
        1.02         0.99        20.94        10.98         1.94 

$`ZIM3 WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 
       15.85        10.62        13.55        12.72        10.39         1.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3726 TCGA-AG-3727 
        1.02         2.01         1.02         0.99         1.02         0.95 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
        0.99         0.92         0.99         1.02         1.02         1.02 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        1.02        13.91         6.02        25.94        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.91        13.02         1.02        12.00        70.03        63.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       49.94        38.93        61.94        40.96        38.01        72.07 

  ZIM3 MUTATED ZIM3 WILD-TYPE 
          0.99           0.92 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
         20.94          72.07 
  ZIM3 MUTATED ZIM3 WILD-TYPE 
          1.94          11.31 
[1] "1.0 - 20.9 (1.9)"  "0.9 - 72.1 (11.3)"
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED"   "ZIM3 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A036 
"ZIM3 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED"   "ZIM3 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A036 
"ZIM3 WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3581     TCGA-AG-3582     TCGA-AG-3583 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3587     TCGA-AG-3599     TCGA-AG-3726     TCGA-AG-3727 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-3878     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED"   "ZIM3 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3999     TCGA-AG-4001     TCGA-AG-4007 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008     TCGA-AG-A00C 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011     TCGA-AG-A014 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L     TCGA-AG-A01W 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025     TCGA-AG-A026 
"ZIM3 WILD-TYPE"   "ZIM3 MUTATED" "ZIM3 WILD-TYPE"   "ZIM3 MUTATED" 
    TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X     TCGA-AG-A032 
"ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" "ZIM3 WILD-TYPE" 
    TCGA-AG-A036 
"ZIM3 WILD-TYPE" 
[1] "hr=" "8.6"
D16V2, continuous
D16V3, binary
                cls
clus              0  1
  ZIM3 MUTATED    2  3
  ZIM3 WILD-TYPE 28 36
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      2    3
  ZIM3 WILD-TYPE   28   36
        clus
vv       ZIM3 MUTATED ZIM3 WILD-TYPE
  FEMALE            2             28
  MALE              3             36
D16V4, binary
                cls
clus              0  1
  ZIM3 MUTATED    4  1
  ZIM3 WILD-TYPE 53  7
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      4    1
  ZIM3 WILD-TYPE   53    7
                                clus
vv                               ZIM3 MUTATED ZIM3 WILD-TYPE
  RECTAL ADENOCARCINOMA                     4             53
  RECTAL MUCINOUS ADENOCARCINOMA            1              7
                vv
clus             T1 T2 T3+T4
  ZIM3 MUTATED    1  1     3
  ZIM3 WILD-TYPE  4 13    47
D16V5, multiclass
       clus
vv      ZIM3 MUTATED ZIM3 WILD-TYPE
  T1               1              4
  T2               1             13
  T3+T4            3             47
                vv
clus             N0 N1 N2
  ZIM3 MUTATED    3  2  0
  ZIM3 WILD-TYPE 40 12 12
D16V6, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  N0            3             40
  N1            2             12
  N2            0             12
D16V7, binary
                cls
clus              0  1
  ZIM3 MUTATED    5  0
  ZIM3 WILD-TYPE 54 10
[1] "tbl2"
                cls
clus             [,1] [,2]
  ZIM3 MUTATED      5    0
  ZIM3 WILD-TYPE   54   10
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  M0            5             54
  M1            0             10
                vv
clus              I II III IV
  ZIM3 MUTATED    2  1   2  0
  ZIM3 WILD-TYPE 16 24  14  8
D16V8, multiclass
     clus
vv    ZIM3 MUTATED ZIM3 WILD-TYPE
  I              2             16
  II             1             24
  III            2             14
  IV             0              8
                vv
clus             R0 R1 R2
  ZIM3 MUTATED    4  1  0
  ZIM3 WILD-TYPE 55  0  8
D16V9, multiclass
    clus
vv   ZIM3 MUTATED ZIM3 WILD-TYPE
  R0            4             55
  R1            1              0
  R2            0              8
D16V10, continuous
                       V1.D                          V2 
            "Time to Death"                       "AGE" 
                         V3                          V4 
                   "GENDER"         "HISTOLOGICAL.TYPE" 
                         V5                          V6 
              "PATHOLOGY.T"               "PATHOLOGY.N" 
                         V7                          V8 
      "PATHOLOGICSPREAD(M)"               "TUMOR.STAGE" 
                         V9                         V10 
"COMPLETENESS.OF.RESECTION"     "NUMBER.OF.LYMPH.NODES" 
> q(save="no")
