
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/423417/COAD-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/COAD-TP/3350202/COAD-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=846, in cluster file=155, common to both=155
[1]  15 155
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
          103            52 
  APC MUTATED APC WILD-TYPE 
          103            52 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              129 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              26              129 
[1] "BRAF MUTATION ANALYSIS"
[1] 3
  BRAF MUTATED BRAF WILD-TYPE 
            20            135 
  BRAF MUTATED BRAF WILD-TYPE 
            20            135 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            58             97 
  KRAS MUTATED KRAS WILD-TYPE 
            58             97 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            75             80 
  TP53 MUTATED TP53 WILD-TYPE 
            75             80 
[1] "FBXW7 MUTATION ANALYSIS"
[1] 3
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             126 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             29             126 
[1] "NRAS MUTATION ANALYSIS"
[1] 3
  NRAS MUTATED NRAS WILD-TYPE 
            15            140 
  NRAS MUTATED NRAS WILD-TYPE 
            15            140 
[1] "SMAD4 MUTATION ANALYSIS"
[1] 3
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             137 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
             18             137 
[1] "FAM123B MUTATION ANALYSIS"
[1] 3
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               136 
  FAM123B MUTATED FAM123B WILD-TYPE 
               19               136 
[1] "SOX9 MUTATION ANALYSIS"
[1] 3
  SOX9 MUTATED SOX9 WILD-TYPE 
             9            146 
  SOX9 MUTATED SOX9 WILD-TYPE 
             9            146 
[1] "ACVR2A MUTATION ANALYSIS"
[1] 3
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               8              147 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               8              147 
[1] "TNFRSF10C MUTATION ANALYSIS"
[1] 3
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 149 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  6                 149 
[1] "SMAD2 MUTATION ANALYSIS"
[1] 3
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             145 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
             10             145 
[1] "ACOT4 MUTATION ANALYSIS"
[1] 3
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             152 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              3             152 
[1] "PCBP1 MUTATION ANALYSIS"
[1] 3
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             151 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              4             151 
[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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "COMPLETENESS.OF.RESECTION"             
[15] "NUMBER.OF.LYMPH.NODES"                 
[16] "TUMOR.STAGECODE"                       
[17] "NEOPLASM.DISEASESTAGE"                 
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 155 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
         423          503          523          447          541          437 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3514 TCGA-AA-3516 
         472          332          278          246           NA           NA 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 
          NA           31           NA           NA           NA           NA 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 
          NA           NA           30           NA           NA           NA 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
          30           NA           NA           NA           NA           31 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3678 
          NA           NA           NA           NA           NA           NA 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 TCGA-AA-3688 
          30           NA           NA           NA           30           NA 
TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
          NA           NA           NA           NA           31           30 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
          30           NA           NA           NA           NA           NA 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
          NA           NA           31           31           28           NA 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
          30           30           NA           NA           NA           31 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
          NA           30           NA           NA           NA           NA 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 
          NA           NA           NA           NA           NA           30 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 
          NA           30           31           30           30           NA 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
          NA           NA           61           NA           NA           NA 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3980 TCGA-AA-3982 
          30           NA           31           NA           NA           NA 
TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
          NA           30           NA           NA          424          548 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
         578          913         1035          548          548          517 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
          NA          822          822           30          517          456 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
         669          638          457           30          396          365 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
         365          396           NA           31         1065           31 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 TCGA-AA-A024 
        1005         1065          791          638           NA           NA 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        1580         1215           NA           NA           28         1246 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
        1215           NA         1245           NA           NA 
Variable 1:'AGE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	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=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "HISTOLOGICAL.TYPE"         "DISTANT.METASTASIS"       
[5] "LYMPH.NODE.METASTASIS"     "COMPLETENESS.OF.RESECTION"
[7] "NUMBER.OF.LYMPH.NODES"     "TUMOR.STAGECODE"          
[9] "NEOPLASM.DISEASESTAGE"    
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 T1  T2  T3  T4 
  4  33 103  15 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 155 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=46, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=5, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=16, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=10, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  APC MUTATED   45  9
  APC WILD-TYPE 24  2
  APC MUTATED APC WILD-TYPE 
           54            26 
  APC MUTATED APC WILD-TYPE 
            9             2 
$`APC MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3555 
       17.19        17.79        10.92         9.14         8.09         0.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3715 
        1.02         2.01         0.99         0.99         1.02         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 
        0.99         1.02         0.99         0.99         1.02         0.99 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3975 TCGA-AA-3977 
        0.99         1.02         0.99         2.01         0.99         1.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       18.02        19.00        18.02        18.02        17.00         4.01 
TCGA-AA-A00O TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       27.02        17.00        14.99        21.99        20.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       13.02        12.00        13.02         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        20.98        39.06        51.95        39.95 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03F TCGA-AY-4071 
        2.01         5.03         0.92        40.96        18.02         0.95 

$`APC WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-AA-3518 
       13.91        16.54        14.70        14.37        15.52         1.02 
TCGA-AA-3526 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3877 TCGA-AA-3949 
        0.99         0.99         1.02         0.92         0.99         0.99 
TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q 
        2.01         0.99        13.94        30.02        34.03        27.02 
TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02Y 
        0.99         0.99        12.00        38.07        26.01        39.95 
TCGA-AA-A03J TCGA-AY-4070 
       40.93        16.31 

  APC MUTATED APC WILD-TYPE 
         0.92          0.92 
  APC MUTATED APC WILD-TYPE 
        51.95         40.93 
  APC MUTATED APC WILD-TYPE 
        8.615        13.925 
[1] "0.9 - 52.0 (8.6)"  "0.9 - 40.9 (13.9)"
   TCGA-A6-2670    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3810 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3518    TCGA-AA-3526    TCGA-AA-3555    TCGA-AA-3562    TCGA-AA-3666 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3679    TCGA-AA-3685    TCGA-AA-3710    TCGA-AA-3715    TCGA-AA-3811 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3818    TCGA-AA-3837    TCGA-AA-3842    TCGA-AA-3844    TCGA-AA-3846 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3848    TCGA-AA-3854    TCGA-AA-3856    TCGA-AA-3877    TCGA-AA-3939 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3941    TCGA-AA-3947    TCGA-AA-3949    TCGA-AA-3952    TCGA-AA-3966 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3975    TCGA-AA-3977    TCGA-AA-3986    TCGA-AA-A004    TCGA-AA-A00A 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-A00D    TCGA-AA-A00E    TCGA-AA-A00F    TCGA-AA-A00J    TCGA-AA-A00K 
  "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A00L    TCGA-AA-A00N    TCGA-AA-A00O    TCGA-AA-A00Q    TCGA-AA-A00R 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-AA-A00U    TCGA-AA-A00W    TCGA-AA-A00Z    TCGA-AA-A010    TCGA-AA-A017 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01D    TCGA-AA-A01F    TCGA-AA-A01G    TCGA-AA-A01I    TCGA-AA-A01K 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01P    TCGA-AA-A01Q    TCGA-AA-A01R    TCGA-AA-A01S    TCGA-AA-A01T 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01V    TCGA-AA-A01X    TCGA-AA-A01Z    TCGA-AA-A024    TCGA-AA-A029 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02F    TCGA-AA-A02H    TCGA-AA-A02J    TCGA-AA-A02O    TCGA-AA-A02W 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02Y    TCGA-AA-A03F    TCGA-AA-A03J    TCGA-AY-4070    TCGA-AY-4071 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-A6-2670    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3810 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3518    TCGA-AA-3526    TCGA-AA-3555    TCGA-AA-3562    TCGA-AA-3666 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3679    TCGA-AA-3685    TCGA-AA-3710    TCGA-AA-3715    TCGA-AA-3811 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3818    TCGA-AA-3837    TCGA-AA-3842    TCGA-AA-3844    TCGA-AA-3846 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3848    TCGA-AA-3854    TCGA-AA-3856    TCGA-AA-3877    TCGA-AA-3939 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3941    TCGA-AA-3947    TCGA-AA-3949    TCGA-AA-3952    TCGA-AA-3966 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3975    TCGA-AA-3977    TCGA-AA-3986    TCGA-AA-A004    TCGA-AA-A00A 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-A00D    TCGA-AA-A00E    TCGA-AA-A00F    TCGA-AA-A00J    TCGA-AA-A00K 
  "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A00L    TCGA-AA-A00N    TCGA-AA-A00O    TCGA-AA-A00Q    TCGA-AA-A00R 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-AA-A00U    TCGA-AA-A00W    TCGA-AA-A00Z    TCGA-AA-A010    TCGA-AA-A017 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01D    TCGA-AA-A01F    TCGA-AA-A01G    TCGA-AA-A01I    TCGA-AA-A01K 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01P    TCGA-AA-A01Q    TCGA-AA-A01R    TCGA-AA-A01S    TCGA-AA-A01T 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01V    TCGA-AA-A01X    TCGA-AA-A01Z    TCGA-AA-A024    TCGA-AA-A029 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02F    TCGA-AA-A02H    TCGA-AA-A02J    TCGA-AA-A02O    TCGA-AA-A02W 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02Y    TCGA-AA-A03F    TCGA-AA-A03J    TCGA-AY-4070    TCGA-AY-4071 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-A6-2670    TCGA-A6-2672    TCGA-A6-2674    TCGA-A6-2676    TCGA-A6-2677 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-A6-2678    TCGA-A6-2683    TCGA-A6-3807    TCGA-A6-3808    TCGA-A6-3810 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3518    TCGA-AA-3526    TCGA-AA-3555    TCGA-AA-3562    TCGA-AA-3666 
"APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-3679    TCGA-AA-3685    TCGA-AA-3710    TCGA-AA-3715    TCGA-AA-3811 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3818    TCGA-AA-3837    TCGA-AA-3842    TCGA-AA-3844    TCGA-AA-3846 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3848    TCGA-AA-3854    TCGA-AA-3856    TCGA-AA-3877    TCGA-AA-3939 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-3941    TCGA-AA-3947    TCGA-AA-3949    TCGA-AA-3952    TCGA-AA-3966 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AA-3975    TCGA-AA-3977    TCGA-AA-3986    TCGA-AA-A004    TCGA-AA-A00A 
  "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
   TCGA-AA-A00D    TCGA-AA-A00E    TCGA-AA-A00F    TCGA-AA-A00J    TCGA-AA-A00K 
  "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A00L    TCGA-AA-A00N    TCGA-AA-A00O    TCGA-AA-A00Q    TCGA-AA-A00R 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE" 
   TCGA-AA-A00U    TCGA-AA-A00W    TCGA-AA-A00Z    TCGA-AA-A010    TCGA-AA-A017 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01D    TCGA-AA-A01F    TCGA-AA-A01G    TCGA-AA-A01I    TCGA-AA-A01K 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01P    TCGA-AA-A01Q    TCGA-AA-A01R    TCGA-AA-A01S    TCGA-AA-A01T 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A01V    TCGA-AA-A01X    TCGA-AA-A01Z    TCGA-AA-A024    TCGA-AA-A029 
  "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02F    TCGA-AA-A02H    TCGA-AA-A02J    TCGA-AA-A02O    TCGA-AA-A02W 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AA-A02Y    TCGA-AA-A03F    TCGA-AA-A03J    TCGA-AY-4070    TCGA-AY-4071 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE" "APC WILD-TYPE"   "APC MUTATED" 
[1] "hr=" "2.3"
D1V2, continuous
D1V3, binary
               cls
clus             0  1
  APC MUTATED   45 58
  APC WILD-TYPE 32 20
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     45   58
  APC WILD-TYPE   32   20
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          45            32
  MALE            58            20
D1V4, binary
               cls
clus             0  1
  APC MUTATED   86 15
  APC WILD-TYPE 43  9
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     86   15
  APC WILD-TYPE   43    9
                               clus
vv                              APC MUTATED APC WILD-TYPE
  COLON ADENOCARCINOMA                   86            43
  COLON MUCINOUS ADENOCARCINOMA          15             9
               vv
clus            M0 M1 M1A
  APC MUTATED   83 17   1
  APC WILD-TYPE 48  4   0
D1V5, multiclass
     clus
vv    APC MUTATED APC WILD-TYPE
  M0           83            48
  M1           17             4
  M1A           1             0
               vv
clus            N0 N1 N1B N2 N2A
  APC MUTATED   61 18   1 23   0
  APC WILD-TYPE 30 11   0 10   1
D1V6, multiclass
               vv
clus            R0 R1 R2 RX
  APC MUTATED   84  0 16  0
  APC WILD-TYPE 45  1  3  1
D1V7, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          84            45
  R1           0             1
  R2          16             3
  RX           0             1
D1V8, continuous
D1V9, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  APC MUTATED        20       10        26         3         8          1
  APC WILD-TYPE      11        4        13         1         6          1
               vv
clus            STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  APC MUTATED            6         10       17         1
  APC WILD-TYPE          6          6        4         0
D1V10, multiclass

Clustering(2) Variable = PIK3CA MUTATION ANALYSIS
D2V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED   15  3
  PIK3CA WILD-TYPE 54  8
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              18               62 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               3                8 
$`PIK3CA MUTATED`
TCGA-A6-3808 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3877 
        9.14         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A010 TCGA-AA-A01I 
        0.99         0.99         1.02         4.01        20.98        12.00 
TCGA-AA-A01K TCGA-AA-A01V TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       13.02        35.01         0.92        39.95        18.02        40.93 

$`PIK3CA WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       15.52        10.92         8.09         1.02         0.99         0.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 
        1.02         2.01         0.99         0.99         1.02         0.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 
        1.02         0.92         0.99         1.02         0.99         1.02 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3986 TCGA-AA-A004 
        0.99         2.01         2.01         0.99         0.99        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       18.02        19.00        30.02        34.03        18.02        18.02 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.00        27.02        27.02         0.99        17.00        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01P 
       21.99        15.02         0.99        13.02        12.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        26.01        20.98 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       39.06        51.95        39.95         2.01         5.03        40.96 
TCGA-AY-4070 TCGA-AY-4071 
       16.31         0.95 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            0.92             0.92 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           40.93            51.95 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           2.515           13.465 
[1] "0.9 - 40.9 (2.5)"  "0.9 - 52.0 (13.5)"
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED"   "PIK3CA MUTATED" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED"   "PIK3CA MUTATED" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED"   "PIK3CA MUTATED" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
  "PIK3CA MUTATED"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
[1] "hr=" "1.4"
D2V2, continuous
D2V3, binary
                  cls
clus                0  1
  PIK3CA MUTATED   12 14
  PIK3CA WILD-TYPE 65 64
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     12   14
  PIK3CA WILD-TYPE   65   64
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE             12               65
  MALE               14               64
D2V4, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    19   7
  PIK3CA WILD-TYPE 110  17
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     19    7
  PIK3CA WILD-TYPE  110   17
                               clus
vv                              PIK3CA MUTATED PIK3CA WILD-TYPE
  COLON ADENOCARCINOMA                      19              110
  COLON MUCINOUS ADENOCARCINOMA              7               17
                  vv
clus                M0  M1 M1A
  PIK3CA MUTATED    24   1   0
  PIK3CA WILD-TYPE 107  20   1
D2V5, multiclass
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              24              107
  M1               1               20
  M1A              0                1
                  vv
clus               N0 N1 N1B N2 N2A
  PIK3CA MUTATED   22  1   0  3   0
  PIK3CA WILD-TYPE 69 28   1 30   1
D2V6, multiclass
                  vv
clus                R0  R1  R2  RX
  PIK3CA MUTATED    24   0   1   0
  PIK3CA WILD-TYPE 105   1  18   1
D2V7, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  R0             24              105
  R1              0                1
  R2              1               18
  RX              0                1
D2V8, continuous
D2V9, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PIK3CA MUTATED         7        4         7         3         1          0
  PIK3CA WILD-TYPE      24       10        32         1        13          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PIK3CA MUTATED            0          2        1         0
  PIK3CA WILD-TYPE         12         14       20         1
D2V10, multiclass

Clustering(3) Variable = BRAF MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  BRAF MUTATED   10  1
  BRAF WILD-TYPE 59 10
  BRAF MUTATED BRAF WILD-TYPE 
            11             69 
  BRAF MUTATED BRAF WILD-TYPE 
             1             10 
$`BRAF MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-AA-3715 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 
       16.54        14.70         0.99         0.99         0.99         0.99 
TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00J TCGA-AA-A01D TCGA-AA-A01P 
        2.01        19.00        18.02         0.99        38.07 

$`BRAF WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       13.91        17.19        17.79        14.37        15.52        10.92 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3562 
        9.14         8.09         1.02         0.99         0.99         1.02 
TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 
        2.01         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
        1.02         1.02         0.92         0.99         0.99         1.02 
TCGA-AA-3856 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3975 TCGA-AA-3977 
        0.99         0.99         1.02         2.01         0.99         1.02 
TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
        0.99        13.94        18.02        30.02        34.03        18.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.00         4.01        27.02        27.02         0.99        17.00 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        20.98        15.02        13.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        13.02         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        20.98        39.06        51.95        39.95 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        40.96        39.95        18.02 
TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       40.93        16.31         0.95 

  BRAF MUTATED BRAF WILD-TYPE 
          0.99           0.92 
  BRAF MUTATED BRAF WILD-TYPE 
         38.07          51.95 
  BRAF MUTATED BRAF WILD-TYPE 
          2.01          12.00 
[1] "1.0 - 38.1 (2.0)"  "0.9 - 52.0 (12.0)"
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "BRAF MUTATED" "BRAF WILD-TYPE"   "BRAF MUTATED" "BRAF WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE"   "BRAF MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
  "BRAF MUTATED" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" "BRAF WILD-TYPE" 
[1] "hr=" "1.3"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  BRAF MUTATED   14  6
  BRAF WILD-TYPE 63 72
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED     14    6
  BRAF WILD-TYPE   63   72
        clus
vv       BRAF MUTATED BRAF WILD-TYPE
  FEMALE           14             63
  MALE              6             72
D3V4, binary
                cls
clus               0   1
  BRAF MUTATED     9  11
  BRAF WILD-TYPE 120  13
[1] "tbl2"
                cls
clus             [,1] [,2]
  BRAF MUTATED      9   11
  BRAF WILD-TYPE  120   13
                               clus
vv                              BRAF MUTATED BRAF WILD-TYPE
  COLON ADENOCARCINOMA                     9            120
  COLON MUCINOUS ADENOCARCINOMA           11             13
                vv
clus              M0  M1 M1A
  BRAF MUTATED    19   1   0
  BRAF WILD-TYPE 112  20   1
D3V5, multiclass
     clus
vv    BRAF MUTATED BRAF WILD-TYPE
  M0            19            112
  M1             1             20
  M1A            0              1
                vv
clus             N0 N1 N1B N2 N2A
  BRAF MUTATED   11  5   0  4   0
  BRAF WILD-TYPE 80 24   1 29   1
D3V6, multiclass
                vv
clus              R0  R1  R2  RX
  BRAF MUTATED    17   0   1   0
  BRAF WILD-TYPE 112   1  18   1
D3V7, multiclass
    clus
vv   BRAF MUTATED BRAF WILD-TYPE
  R0           17            112
  R1            0              1
  R2            1             18
  RX            0              1
D3V8, continuous
D3V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  BRAF MUTATED         4        3         2         2         2          0
  BRAF WILD-TYPE      27       11        37         2        12          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  BRAF MUTATED            4          2        1         0
  BRAF WILD-TYPE          8         14       20         1
D3V10, multiclass

Clustering(4) Variable = KRAS MUTATION ANALYSIS
D4V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   30  3
  KRAS WILD-TYPE 39  8
  KRAS MUTATED KRAS WILD-TYPE 
            33             47 
  KRAS MUTATED KRAS WILD-TYPE 
             3              8 
$`KRAS MUTATED`
TCGA-A6-2683 TCGA-A6-3808 TCGA-AA-3555 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 
       15.52         9.14         0.99         0.99         0.99         1.02 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3939 TCGA-AA-3941 
        1.02         0.92         0.99         1.02         0.99         1.02 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A00A TCGA-AA-A00K TCGA-AA-A00N 
        0.99         1.02         0.99        18.02        18.02         4.01 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       27.02        14.99        13.02        12.00        12.00        13.02 
TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W 
       35.01        26.01        20.98        51.95         0.92        40.96 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.95        18.02        40.93 

$`KRAS WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3562 TCGA-AA-3666 
       10.92         8.09         1.02         0.99         1.02         2.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3846 TCGA-AA-3856 
        0.99         0.99         1.02         0.99         0.99         0.99 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-A004 
        0.99         0.99         0.99         2.01         2.01        13.94 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O 
       19.00        30.02        34.03        18.02        17.00        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.00        21.99        20.98        15.02         0.99 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A024 
       38.07         1.02         1.02        33.04        35.01        39.06 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AY-4070 TCGA-AY-4071 
       39.95         2.01         5.03        16.31         0.95 

  KRAS MUTATED KRAS WILD-TYPE 
          0.92           0.95 
  KRAS MUTATED KRAS WILD-TYPE 
         51.95          39.95 
  KRAS MUTATED KRAS WILD-TYPE 
         12.00          10.92 
[1] "0.9 - 52.0 (12.0)" "0.9 - 40.0 (10.9)"
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
  "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
[1] "hr=" "2.2"
D4V2, continuous
D4V3, binary
                cls
clus              0  1
  KRAS MUTATED   25 33
  KRAS WILD-TYPE 52 45
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     25   33
  KRAS WILD-TYPE   52   45
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           25             52
  MALE             33             45
D4V4, binary
                cls
clus              0  1
  KRAS MUTATED   47 10
  KRAS WILD-TYPE 82 14
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     47   10
  KRAS WILD-TYPE   82   14
                               clus
vv                              KRAS MUTATED KRAS WILD-TYPE
  COLON ADENOCARCINOMA                    47             82
  COLON MUCINOUS ADENOCARCINOMA           10             14
                vv
clus             M0 M1 M1A
  KRAS MUTATED   50  6   1
  KRAS WILD-TYPE 81 15   0
D4V5, multiclass
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  M0            50             81
  M1             6             15
  M1A            1              0
                vv
clus             N0 N1 N1B N2 N2A
  KRAS MUTATED   38  8   1 11   0
  KRAS WILD-TYPE 53 21   0 22   1
D4V6, multiclass
                vv
clus             R0 R1 R2 RX
  KRAS MUTATED   51  0  5  1
  KRAS WILD-TYPE 78  1 14  0
D4V7, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           51             78
  R1            0              1
  R2            5             14
  RX            1              0
D4V8, continuous
D4V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  KRAS MUTATED        11        8        16         1         5          1
  KRAS WILD-TYPE      20        6        23         3         9          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  KRAS MUTATED            3          5        6         1
  KRAS WILD-TYPE          9         11       15         0
D4V10, multiclass

Clustering(5) Variable = TP53 MUTATION ANALYSIS
D5V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   38  5
  TP53 WILD-TYPE 31  6
  TP53 MUTATED TP53 WILD-TYPE 
            43             37 
  TP53 MUTATED TP53 WILD-TYPE 
             5              6 
$`TP53 MUTATED`
TCGA-A6-2670 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 
       13.91        17.19        14.70        14.37        15.52        10.92 
TCGA-A6-3810 TCGA-AA-3526 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 
        8.09         0.99         1.02         2.01         0.99         0.99 
TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3941 
        0.99         1.02         0.92         0.99         0.99         1.02 
TCGA-AA-3949 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
        0.99         0.99         1.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01D 
       34.03        17.00        27.02        14.99        20.98         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       13.02        12.00        13.02         1.02        33.04        20.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AY-4070 
       39.95         2.01         5.03        40.96        40.93        16.31 
TCGA-AY-4071 
        0.95 

$`TP53 WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-3808 TCGA-AA-3518 TCGA-AA-3555 TCGA-AA-3710 
       16.54        17.79         9.14         1.02         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3877 
        0.99         0.99         1.02         0.99         1.02         0.99 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3986 TCGA-AA-A00A 
        0.99         0.99         2.01         2.01         0.99        18.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.02        18.02         4.01        27.02         0.99        17.00 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       21.99        15.02        12.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y 
       35.01        26.01        39.06        51.95         0.92        39.95 
TCGA-AA-A03F 
       18.02 

  TP53 MUTATED TP53 WILD-TYPE 
          0.92           0.92 
  TP53 MUTATED TP53 WILD-TYPE 
         40.96          51.95 
  TP53 MUTATED TP53 WILD-TYPE 
         12.00           9.14 
[1] "0.9 - 41.0 (12.0)" "0.9 - 52.0 (9.1)" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
  "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
                cls
clus              0  1
  TP53 MUTATED   34 41
  TP53 WILD-TYPE 43 37
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     34   41
  TP53 WILD-TYPE   43   37
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           34             43
  MALE             41             37
D5V4, binary
                cls
clus              0  1
  TP53 MUTATED   68  5
  TP53 WILD-TYPE 61 19
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     68    5
  TP53 WILD-TYPE   61   19
                               clus
vv                              TP53 MUTATED TP53 WILD-TYPE
  COLON ADENOCARCINOMA                    68             61
  COLON MUCINOUS ADENOCARCINOMA            5             19
                vv
clus             M0 M1 M1A
  TP53 MUTATED   61 11   1
  TP53 WILD-TYPE 70 10   0
D5V5, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  M0            61             70
  M1            11             10
  M1A            1              0
                vv
clus             N0 N1 N1B N2 N2A
  TP53 MUTATED   39 15   1 19   1
  TP53 WILD-TYPE 52 14   0 14   0
D5V6, multiclass
                vv
clus             R0 R1 R2 RX
  TP53 MUTATED   61  1 10  0
  TP53 WILD-TYPE 68  0  9  1
D5V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           61             68
  R1            1              0
  R2           10              9
  RX            0              1
D5V8, continuous
D5V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TP53 MUTATED        16        4        14         2         6          2
  TP53 WILD-TYPE      15       10        25         2         8          0
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TP53 MUTATED            6         12       11         1
  TP53 WILD-TYPE          6          4       10         0
D5V10, multiclass

Clustering(6) Variable = FBXW7 MUTATION ANALYSIS
D6V1, survival
                 sevent
clus2              0  1
  FBXW7 MUTATED   13  2
  FBXW7 WILD-TYPE 56  9
  FBXW7 MUTATED FBXW7 WILD-TYPE 
             15              65 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
              2               9 
$`FBXW7 MUTATED`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-3807 TCGA-AA-3518 TCGA-AA-3837 
       16.54        14.70        17.79        10.92         1.02         1.02 
TCGA-AA-3848 TCGA-AA-3949 TCGA-AA-A00J TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01R 
        0.99         0.99        18.02        13.02         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A03F 
       20.98        39.06        18.02 

$`FBXW7 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3808 TCGA-A6-3810 
       13.91        17.19        14.37        15.52         9.14         8.09 
TCGA-AA-3526 TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 
        0.99         0.99         1.02         2.01         0.99         0.99 
TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3844 
        1.02         0.99         0.99         0.99         1.02         0.92 
TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
        0.99         1.02         0.99         0.99         0.99         1.02 
TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 
        0.99         2.01         2.01         0.99         1.02         0.99 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K 
       13.94        18.02        19.00        30.02        34.03        18.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.00         4.01        27.02        27.02         0.99        17.00 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        20.98        15.02         0.99        13.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       12.00        12.00        38.07         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        51.95        39.95         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       40.96        39.95        40.93        16.31         0.95 

  FBXW7 MUTATED FBXW7 WILD-TYPE 
           0.99            0.92 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          39.06           51.95 
  FBXW7 MUTATED FBXW7 WILD-TYPE 
          14.70            8.09 
[1] "1.0 - 39.1 (14.7)" "0.9 - 52.0 (8.1)" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"FBXW7 WILD-TYPE"   "FBXW7 MUTATED"   "FBXW7 MUTATED" "FBXW7 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE"   "FBXW7 MUTATED" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
  "FBXW7 MUTATED" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" "FBXW7 WILD-TYPE" 
[1] "hr=" "1.1"
D6V2, continuous
D6V3, binary
                 cls
clus               0  1
  FBXW7 MUTATED   18 11
  FBXW7 WILD-TYPE 59 67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     18   11
  FBXW7 WILD-TYPE   59   67
        clus
vv       FBXW7 MUTATED FBXW7 WILD-TYPE
  FEMALE            18              59
  MALE              11              67
D6V4, binary
                 cls
clus                0   1
  FBXW7 MUTATED    19  10
  FBXW7 WILD-TYPE 110  14
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FBXW7 MUTATED     19   10
  FBXW7 WILD-TYPE  110   14
                               clus
vv                              FBXW7 MUTATED FBXW7 WILD-TYPE
  COLON ADENOCARCINOMA                     19             110
  COLON MUCINOUS ADENOCARCINOMA            10              14
                 vv
clus               M0  M1 M1A
  FBXW7 MUTATED    29   0   0
  FBXW7 WILD-TYPE 102  21   1
D6V5, multiclass
     clus
vv    FBXW7 MUTATED FBXW7 WILD-TYPE
  M0             29             102
  M1              0              21
  M1A             0               1
                 vv
clus              N0 N1 N1B N2 N2A
  FBXW7 MUTATED   15  6   0  8   0
  FBXW7 WILD-TYPE 76 23   1 25   1
D6V6, multiclass
                 vv
clus               R0  R1  R2  RX
  FBXW7 MUTATED    27   0   0   0
  FBXW7 WILD-TYPE 102   1  19   1
D6V7, multiclass
    clus
vv   FBXW7 MUTATED FBXW7 WILD-TYPE
  R0            27             102
  R1             0               1
  R2             0              19
  RX             0               1
D6V8, continuous
D6V9, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FBXW7 MUTATED         2        5         7         1         5          0
  FBXW7 WILD-TYPE      29        9        32         3         9          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FBXW7 MUTATED            4          5        0         0
  FBXW7 WILD-TYPE          8         11       21         1
D6V10, multiclass

Clustering(7) Variable = NRAS MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  NRAS MUTATED    4  3
  NRAS WILD-TYPE 65  8
  NRAS MUTATED NRAS WILD-TYPE 
             7             73 
  NRAS MUTATED NRAS WILD-TYPE 
             3              8 
$`NRAS MUTATED`
TCGA-A6-2678 TCGA-AA-3666 TCGA-AA-A00F TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 
       14.37         2.01        34.03         4.01        35.01        39.06 
TCGA-AA-A02F 
       39.95 

$`NRAS WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2683 
       13.91        16.54        17.19        14.70        17.79        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       10.92         9.14         8.09         1.02         0.99         0.99 
TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
        1.02         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99         1.02         1.02         0.92         0.99         0.99 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
        1.02         0.99         0.99         0.99         1.02         0.99 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 
        0.99         2.01         2.01         0.99         1.02         0.99 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        18.02        19.00        30.02        18.02        18.02 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.00        27.02        27.02         0.99        17.00        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       21.99        20.98        15.02         0.99        13.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        13.02        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01        20.98        51.95         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        40.96        39.95        18.02        40.93        16.31 
TCGA-AY-4071 
        0.95 

  NRAS MUTATED NRAS WILD-TYPE 
          2.01           0.92 
  NRAS MUTATED NRAS WILD-TYPE 
         39.95          51.95 
  NRAS MUTATED NRAS WILD-TYPE 
         34.03           9.14 
[1] "2.0 - 40.0 (34.0)" "0.9 - 52.0 (9.1)" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
  "NRAS MUTATED" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
  "NRAS MUTATED" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"NRAS WILD-TYPE" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
  "NRAS MUTATED" "NRAS WILD-TYPE"   "NRAS MUTATED" "NRAS WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
"NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" "NRAS WILD-TYPE" 
[1] "hr=" "2"  
D7V2, continuous
D7V3, binary
                cls
clus              0  1
  NRAS MUTATED    3 12
  NRAS WILD-TYPE 74 66
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED      3   12
  NRAS WILD-TYPE   74   66
        clus
vv       NRAS MUTATED NRAS WILD-TYPE
  FEMALE            3             74
  MALE             12             66
D7V4, binary
                cls
clus               0   1
  NRAS MUTATED    13   2
  NRAS WILD-TYPE 116  22
[1] "tbl2"
                cls
clus             [,1] [,2]
  NRAS MUTATED     13    2
  NRAS WILD-TYPE  116   22
                               clus
vv                              NRAS MUTATED NRAS WILD-TYPE
  COLON ADENOCARCINOMA                    13            116
  COLON MUCINOUS ADENOCARCINOMA            2             22
                vv
clus              M0  M1 M1A
  NRAS MUTATED    12   3   0
  NRAS WILD-TYPE 119  18   1
D7V5, multiclass
     clus
vv    NRAS MUTATED NRAS WILD-TYPE
  M0            12            119
  M1             3             18
  M1A            0              1
                vv
clus             N0 N1 N1B N2 N2A
  NRAS MUTATED    8  6   0  1   0
  NRAS WILD-TYPE 83 23   1 32   1
D7V6, multiclass
                vv
clus              R0  R1  R2  RX
  NRAS MUTATED    11   0   4   0
  NRAS WILD-TYPE 118   1  15   1
D7V7, multiclass
    clus
vv   NRAS MUTATED NRAS WILD-TYPE
  R0           11            118
  R1            0              1
  R2            4             15
  RX            0              1
D7V8, continuous
D7V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  NRAS MUTATED         4        2         1         1         1          1
  NRAS WILD-TYPE      27       12        38         3        13          1
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  NRAS MUTATED            1          1        3         0
  NRAS WILD-TYPE         11         15       18         1
D7V10, multiclass

Clustering(8) Variable = SMAD4 MUTATION ANALYSIS
D8V1, survival
                 sevent
clus2              0  1
  SMAD4 MUTATED    7  1
  SMAD4 WILD-TYPE 62 10
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              8              72 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
              1              10 
$`SMAD4 MUTATED`
TCGA-A6-2676 TCGA-A6-2678 TCGA-AA-3555 TCGA-AA-3666 TCGA-AA-3811 TCGA-AA-A00K 
       14.70        14.37         0.99         2.01         0.99        18.02 
TCGA-AA-A01D TCGA-AA-A02O 
        0.99         0.92 

$`SMAD4 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2683 TCGA-A6-3807 
       13.91        16.54        17.19        17.79        15.52        10.92 
TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3562 TCGA-AA-3679 
        9.14         8.09         1.02         0.99         1.02         0.99 
TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 
        0.99         1.02         0.99         0.99         1.02         1.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 
        0.92         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 
        0.99         1.02         0.99         0.99         2.01         2.01 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
        0.99         1.02         0.99        13.94        18.02        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.02        17.00         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.00        14.99        21.99        20.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        13.02        12.00        12.00        13.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       20.98        39.06        51.95        39.95         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       40.96        39.95        18.02        40.93        16.31         0.95 

  SMAD4 MUTATED SMAD4 WILD-TYPE 
           0.92            0.92 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
          18.02           51.95 
  SMAD4 MUTATED SMAD4 WILD-TYPE 
            1.5            12.0 
[1] "0.9 - 18.0 (1.5)"  "0.9 - 52.0 (12.0)"
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
  "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE"   "SMAD4 MUTATED" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD4 WILD-TYPE"   "SMAD4 MUTATED" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" "SMAD4 WILD-TYPE" 
[1] "hr=" "1.7"
D8V2, continuous
D8V3, binary
                 cls
clus               0  1
  SMAD4 MUTATED   10  8
  SMAD4 WILD-TYPE 67 70
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     10    8
  SMAD4 WILD-TYPE   67   70
        clus
vv       SMAD4 MUTATED SMAD4 WILD-TYPE
  FEMALE            10              67
  MALE               8              70
D8V4, binary
                 cls
clus                0   1
  SMAD4 MUTATED    13   5
  SMAD4 WILD-TYPE 116  19
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD4 MUTATED     13    5
  SMAD4 WILD-TYPE  116   19
                               clus
vv                              SMAD4 MUTATED SMAD4 WILD-TYPE
  COLON ADENOCARCINOMA                     13             116
  COLON MUCINOUS ADENOCARCINOMA             5              19
                 vv
clus               M0  M1 M1A
  SMAD4 MUTATED    16   2   0
  SMAD4 WILD-TYPE 115  19   1
D8V5, multiclass
     clus
vv    SMAD4 MUTATED SMAD4 WILD-TYPE
  M0             16             115
  M1              2              19
  M1A             0               1
                 vv
clus              N0 N1 N1B N2 N2A
  SMAD4 MUTATED   12  3   0  3   0
  SMAD4 WILD-TYPE 79 26   1 30   1
D8V6, multiclass
                 vv
clus               R0  R1  R2  RX
  SMAD4 MUTATED    15   0   3   0
  SMAD4 WILD-TYPE 114   1  16   1
D8V7, multiclass
    clus
vv   SMAD4 MUTATED SMAD4 WILD-TYPE
  R0            15             114
  R1             0               1
  R2             3              16
  RX             0               1
D8V8, continuous
D8V9, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD4 MUTATED         3        3         5         1         2          0
  SMAD4 WILD-TYPE      28       11        34         3        12          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD4 MUTATED            1          1        2         0
  SMAD4 WILD-TYPE         11         15       19         1
D8V10, multiclass

Clustering(9) Variable = FAM123B MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  FAM123B MUTATED    6  1
  FAM123B WILD-TYPE 63 10
  FAM123B MUTATED FAM123B WILD-TYPE 
                7                73 
  FAM123B MUTATED FAM123B WILD-TYPE 
                1                10 
$`FAM123B MUTATED`
TCGA-A6-3808 TCGA-AA-3666 TCGA-AA-3939 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A010 
        9.14         2.01         0.99         1.02        18.02        20.98 
TCGA-AA-A01D 
        0.99 

$`FAM123B WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       15.52        10.92         8.09         1.02         0.99         0.99 
TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3811 
        1.02         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99         1.02         1.02         0.92         0.99         0.99 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
        1.02         0.99         0.99         1.02         0.99         0.99 
TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00D 
        2.01         2.01         0.99         0.99        13.94        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.02        18.02        17.00         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        27.02         0.99        17.00        14.99        21.99 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        13.02        12.00        12.00        13.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       20.98        39.06        51.95        39.95         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        40.96        39.95        18.02        40.93        16.31 
TCGA-AY-4071 
        0.95 

  FAM123B MUTATED FAM123B WILD-TYPE 
             0.99              0.92 
  FAM123B MUTATED FAM123B WILD-TYPE 
            20.98             51.95 
  FAM123B MUTATED FAM123B WILD-TYPE 
             2.01             12.00 
[1] "1.0 - 21.0 (2.0)"  "0.9 - 52.0 (12.0)"
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3810        TCGA-AA-3518        TCGA-AA-3526 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3562        TCGA-AA-3666        TCGA-AA-3679 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3854        TCGA-AA-3856 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3952        TCGA-AA-3966        TCGA-AA-3975 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3977        TCGA-AA-3986        TCGA-AA-A004        TCGA-AA-A00A 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3810        TCGA-AA-3518        TCGA-AA-3526 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3562        TCGA-AA-3666        TCGA-AA-3679 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3854        TCGA-AA-3856 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3952        TCGA-AA-3966        TCGA-AA-3975 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3977        TCGA-AA-3986        TCGA-AA-A004        TCGA-AA-A00A 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-2670        TCGA-A6-2672        TCGA-A6-2674        TCGA-A6-2676 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-2677        TCGA-A6-2678        TCGA-A6-2683        TCGA-A6-3807 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-A6-3808        TCGA-A6-3810        TCGA-AA-3518        TCGA-AA-3526 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3555        TCGA-AA-3562        TCGA-AA-3666        TCGA-AA-3679 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" 
       TCGA-AA-3685        TCGA-AA-3710        TCGA-AA-3715        TCGA-AA-3811 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3818        TCGA-AA-3837        TCGA-AA-3842        TCGA-AA-3844 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3846        TCGA-AA-3848        TCGA-AA-3854        TCGA-AA-3856 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3877        TCGA-AA-3939        TCGA-AA-3941        TCGA-AA-3947 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3949        TCGA-AA-3952        TCGA-AA-3966        TCGA-AA-3975 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-3977        TCGA-AA-3986        TCGA-AA-A004        TCGA-AA-A00A 
  "FAM123B MUTATED" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A00D        TCGA-AA-A00E        TCGA-AA-A00F        TCGA-AA-A00J 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00K        TCGA-AA-A00L        TCGA-AA-A00N        TCGA-AA-A00O 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Q        TCGA-AA-A00R        TCGA-AA-A00U        TCGA-AA-A00W 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A00Z        TCGA-AA-A010        TCGA-AA-A017        TCGA-AA-A01D 
"FAM123B WILD-TYPE"   "FAM123B MUTATED" "FAM123B WILD-TYPE"   "FAM123B MUTATED" 
       TCGA-AA-A01F        TCGA-AA-A01G        TCGA-AA-A01I        TCGA-AA-A01K 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01P        TCGA-AA-A01Q        TCGA-AA-A01R        TCGA-AA-A01S 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A01T        TCGA-AA-A01V        TCGA-AA-A01X        TCGA-AA-A01Z 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A024        TCGA-AA-A029        TCGA-AA-A02F        TCGA-AA-A02H 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A02J        TCGA-AA-A02O        TCGA-AA-A02W        TCGA-AA-A02Y 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
       TCGA-AA-A03F        TCGA-AA-A03J        TCGA-AY-4070        TCGA-AY-4071 
"FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" "FAM123B WILD-TYPE" 
[1] "hr=" "1.5"
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  FAM123B MUTATED   10  9
  FAM123B WILD-TYPE 67 69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     10    9
  FAM123B WILD-TYPE   67   69
        clus
vv       FAM123B MUTATED FAM123B WILD-TYPE
  FEMALE              10                67
  MALE                 9                69
D9V4, binary
                   cls
clus                  0   1
  FAM123B MUTATED    15   4
  FAM123B WILD-TYPE 114  20
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM123B MUTATED     15    4
  FAM123B WILD-TYPE  114   20
                               clus
vv                              FAM123B MUTATED FAM123B WILD-TYPE
  COLON ADENOCARCINOMA                       15               114
  COLON MUCINOUS ADENOCARCINOMA               4                20
                   vv
clus                 M0  M1 M1A
  FAM123B MUTATED    16   2   0
  FAM123B WILD-TYPE 115  19   1
D9V5, multiclass
     clus
vv    FAM123B MUTATED FAM123B WILD-TYPE
  M0               16               115
  M1                2                19
  M1A               0                 1
                   vv
clus                N0 N1 N1B N2 N2A
  FAM123B MUTATED   13  1   0  5   0
  FAM123B WILD-TYPE 78 28   1 28   1
D9V6, multiclass
                   vv
clus                 R0  R1  R2  RX
  FAM123B MUTATED    15   0   2   0
  FAM123B WILD-TYPE 114   1  17   1
D9V7, multiclass
    clus
vv   FAM123B MUTATED FAM123B WILD-TYPE
  R0              15               114
  R1               0                 1
  R2               2                17
  RX               0                 1
D9V8, continuous
D9V9, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  FAM123B MUTATED         2        2         7         1         2          0
  FAM123B WILD-TYPE      29       12        32         3        12          2
                   vv
clus                STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  FAM123B MUTATED            0          2        2         0
  FAM123B WILD-TYPE         12         14       19         1
D9V10, multiclass

Clustering(10) Variable = SOX9 MUTATION ANALYSIS
D10V1, survival
                sevent
clus2             0  1
  SOX9 MUTATED    1  1
  SOX9 WILD-TYPE 68 10
  SOX9 MUTATED SOX9 WILD-TYPE 
             2             78 
  SOX9 MUTATED SOX9 WILD-TYPE 
             1             10 
$`SOX9 MUTATED`
TCGA-AA-3939 TCGA-AA-A03F 
        0.99        18.02 

$`SOX9 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 
       15.52        10.92         9.14         8.09         1.02         0.99 
TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 
        0.99         1.02         2.01         0.99         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99         0.99         0.99         1.02         1.02         0.92 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3941 
        0.99         0.99         1.02         0.99         0.99         1.02 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 
        0.99         0.99         2.01         2.01         0.99         1.02 
TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        0.99        13.94        18.02        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.02        18.02        17.00         4.01        27.02        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.00        14.99        21.99        20.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        13.02        12.00        12.00        13.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       20.98        39.06        51.95        39.95         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
        0.92        40.96        39.95        40.93        16.31         0.95 

  SOX9 MUTATED SOX9 WILD-TYPE 
          0.99           0.92 
  SOX9 MUTATED SOX9 WILD-TYPE 
         18.02          51.95 
  SOX9 MUTATED SOX9 WILD-TYPE 
         9.505         11.460 
[1] "1.0 - 18.0 (9.5)"  "0.9 - 52.0 (11.5)"
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"SOX9 WILD-TYPE"   "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"SOX9 WILD-TYPE"   "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3939     TCGA-AA-3941     TCGA-AA-3947 
"SOX9 WILD-TYPE"   "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3949     TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3977     TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00D     TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00K     TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Q     TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00Z     TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01F     TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01P     TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01T     TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A024     TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A02J     TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A03F     TCGA-AA-A03J     TCGA-AY-4070     TCGA-AY-4071 
  "SOX9 MUTATED" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
[1] "Remove cluster labels:" "SOX9 MUTATED"          
clus
  SOX9 MUTATED SOX9 WILD-TYPE 
             2             78 
    TCGA-A6-2670     TCGA-A6-2672     TCGA-A6-2674     TCGA-A6-2676 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-2677     TCGA-A6-2678     TCGA-A6-2683     TCGA-A6-3807 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-A6-3808     TCGA-A6-3810     TCGA-AA-3518     TCGA-AA-3526 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3555     TCGA-AA-3562     TCGA-AA-3666     TCGA-AA-3679 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3685     TCGA-AA-3710     TCGA-AA-3715     TCGA-AA-3811 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3818     TCGA-AA-3837     TCGA-AA-3842     TCGA-AA-3844 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3846     TCGA-AA-3848     TCGA-AA-3854     TCGA-AA-3856 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3877     TCGA-AA-3941     TCGA-AA-3947     TCGA-AA-3949 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3952     TCGA-AA-3966     TCGA-AA-3975     TCGA-AA-3977 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-3986     TCGA-AA-A004     TCGA-AA-A00A     TCGA-AA-A00D 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00E     TCGA-AA-A00F     TCGA-AA-A00J     TCGA-AA-A00K 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00L     TCGA-AA-A00N     TCGA-AA-A00O     TCGA-AA-A00Q 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A00R     TCGA-AA-A00U     TCGA-AA-A00W     TCGA-AA-A00Z 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A010     TCGA-AA-A017     TCGA-AA-A01D     TCGA-AA-A01F 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01G     TCGA-AA-A01I     TCGA-AA-A01K     TCGA-AA-A01P 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01Q     TCGA-AA-A01R     TCGA-AA-A01S     TCGA-AA-A01T 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A01V     TCGA-AA-A01X     TCGA-AA-A01Z     TCGA-AA-A024 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A029     TCGA-AA-A02F     TCGA-AA-A02H     TCGA-AA-A02J 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AA-A02O     TCGA-AA-A02W     TCGA-AA-A02Y     TCGA-AA-A03J 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
    TCGA-AY-4070     TCGA-AY-4071 
"SOX9 WILD-TYPE" "SOX9 WILD-TYPE" 
D10V2, continuous
D10V3, binary
                cls
clus              0  1
  SOX9 MUTATED    5  4
  SOX9 WILD-TYPE 72 74
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED      5    4
  SOX9 WILD-TYPE   72   74
        clus
vv       SOX9 MUTATED SOX9 WILD-TYPE
  FEMALE            5             72
  MALE              4             74
D10V4, binary
                cls
clus               0   1
  SOX9 MUTATED     8   1
  SOX9 WILD-TYPE 121  23
[1] "tbl2"
                cls
clus             [,1] [,2]
  SOX9 MUTATED      8    1
  SOX9 WILD-TYPE  121   23
                               clus
vv                              SOX9 MUTATED SOX9 WILD-TYPE
  COLON ADENOCARCINOMA                     8            121
  COLON MUCINOUS ADENOCARCINOMA            1             23
                vv
clus              M0  M1 M1A
  SOX9 MUTATED     8   1   0
  SOX9 WILD-TYPE 123  20   1
D10V5, multiclass
     clus
vv    SOX9 MUTATED SOX9 WILD-TYPE
  M0             8            123
  M1             1             20
  M1A            0              1
                vv
clus             N0 N1 N1B N2 N2A
  SOX9 MUTATED    6  1   0  2   0
  SOX9 WILD-TYPE 85 28   1 31   1
D10V6, multiclass
                vv
clus              R0  R1  R2  RX
  SOX9 MUTATED     8   0   1   0
  SOX9 WILD-TYPE 121   1  18   1
D10V7, multiclass
    clus
vv   SOX9 MUTATED SOX9 WILD-TYPE
  R0            8            121
  R1            0              1
  R2            1             18
  RX            0              1
D10V8, continuous
D10V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SOX9 MUTATED         0        0         6         0         2          0
  SOX9 WILD-TYPE      31       14        33         4        12          2
                vv
clus             STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SOX9 MUTATED            0          0        1         0
  SOX9 WILD-TYPE         12         16       20         1
D10V10, multiclass

Clustering(11) Variable = ACVR2A MUTATION ANALYSIS
D11V1, survival
                  sevent
clus2               0  1
  ACVR2A MUTATED    6  0
  ACVR2A WILD-TYPE 63 11
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               6               74 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
               0               11 
$`ACVR2A MUTATED`
TCGA-A6-2672 TCGA-AA-3710 TCGA-AA-3966 TCGA-AA-A010 TCGA-AA-A01V TCGA-AA-A02F 
       16.54         1.02         2.01        20.98        35.01        39.95 

$`ACVR2A WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 
       13.91        17.19        14.70        17.79        14.37        15.52 
TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3555 
       10.92         9.14         8.09         1.02         0.99         0.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3715 TCGA-AA-3811 
        1.02         2.01         0.99         0.99         0.99         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99         1.02         1.02         0.92         0.99         0.99 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
        1.02         0.99         0.99         0.99         1.02         0.99 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-A004 
        0.99         2.01         0.99         1.02         0.99        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       18.02        19.00        30.02        34.03        18.02        18.02 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.00         4.01        27.02        27.02         0.99        17.00 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02         0.99        13.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        13.02        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H 
       33.04        26.01        20.98        39.06        51.95         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        40.96        39.95        18.02        40.93 
TCGA-AY-4070 TCGA-AY-4071 
       16.31         0.95 

  ACVR2A MUTATED ACVR2A WILD-TYPE 
            1.02             0.92 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
           39.95            51.95 
  ACVR2A MUTATED ACVR2A WILD-TYPE 
           18.76            10.03 
[1] "1.0 - 40.0 (18.8)" "0.9 - 52.0 (10.0)"
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-2670       TCGA-A6-2672       TCGA-A6-2674       TCGA-A6-2676 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-2677       TCGA-A6-2678       TCGA-A6-2683       TCGA-A6-3807 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-A6-3808       TCGA-A6-3810       TCGA-AA-3518       TCGA-AA-3526 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3555       TCGA-AA-3562       TCGA-AA-3666       TCGA-AA-3679 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3685       TCGA-AA-3710       TCGA-AA-3715       TCGA-AA-3811 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3818       TCGA-AA-3837       TCGA-AA-3842       TCGA-AA-3844 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3846       TCGA-AA-3848       TCGA-AA-3854       TCGA-AA-3856 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3877       TCGA-AA-3939       TCGA-AA-3941       TCGA-AA-3947 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-3949       TCGA-AA-3952       TCGA-AA-3966       TCGA-AA-3975 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-3977       TCGA-AA-3986       TCGA-AA-A004       TCGA-AA-A00A 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00D       TCGA-AA-A00E       TCGA-AA-A00F       TCGA-AA-A00J 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00K       TCGA-AA-A00L       TCGA-AA-A00N       TCGA-AA-A00O 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Q       TCGA-AA-A00R       TCGA-AA-A00U       TCGA-AA-A00W 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A00Z       TCGA-AA-A010       TCGA-AA-A017       TCGA-AA-A01D 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01F       TCGA-AA-A01G       TCGA-AA-A01I       TCGA-AA-A01K 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01P       TCGA-AA-A01Q       TCGA-AA-A01R       TCGA-AA-A01S 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A01T       TCGA-AA-A01V       TCGA-AA-A01X       TCGA-AA-A01Z 
"ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A024       TCGA-AA-A029       TCGA-AA-A02F       TCGA-AA-A02H 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE"   "ACVR2A MUTATED" "ACVR2A WILD-TYPE" 
      TCGA-AA-A02J       TCGA-AA-A02O       TCGA-AA-A02W       TCGA-AA-A02Y 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
      TCGA-AA-A03F       TCGA-AA-A03J       TCGA-AY-4070       TCGA-AY-4071 
"ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" "ACVR2A WILD-TYPE" 
[1] "hr="   "8e+07"
D11V2, continuous
D11V3, binary
                  cls
clus                0  1
  ACVR2A MUTATED    7  1
  ACVR2A WILD-TYPE 70 77
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      7    1
  ACVR2A WILD-TYPE   70   77
        clus
vv       ACVR2A MUTATED ACVR2A WILD-TYPE
  FEMALE              7               70
  MALE                1               77
D11V4, binary
                  cls
clus                 0   1
  ACVR2A MUTATED     7   1
  ACVR2A WILD-TYPE 122  23
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ACVR2A MUTATED      7    1
  ACVR2A WILD-TYPE  122   23
                               clus
vv                              ACVR2A MUTATED ACVR2A WILD-TYPE
  COLON ADENOCARCINOMA                       7              122
  COLON MUCINOUS ADENOCARCINOMA              1               23
                  vv
clus                M0  M1 M1A
  ACVR2A MUTATED     7   1   0
  ACVR2A WILD-TYPE 124  20   1
D11V5, multiclass
     clus
vv    ACVR2A MUTATED ACVR2A WILD-TYPE
  M0               7              124
  M1               1               20
  M1A              0                1
                  vv
clus               N0 N1 N1B N2 N2A
  ACVR2A MUTATED    6  2   0  0   0
  ACVR2A WILD-TYPE 85 27   1 33   1
D11V6, multiclass
                  vv
clus                R0  R1  R2  RX
  ACVR2A MUTATED     6   0   1   0
  ACVR2A WILD-TYPE 123   1  18   1
D11V7, multiclass
    clus
vv   ACVR2A MUTATED ACVR2A WILD-TYPE
  R0              6              123
  R1              0                1
  R2              1               18
  RX              0                1
D11V8, continuous
D11V9, continuous
                  vv
clus               STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ACVR2A MUTATED         1        0         4         1         0          0
  ACVR2A WILD-TYPE      30       14        35         3        14          2
                  vv
clus               STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACVR2A MUTATED            1          0        1         0
  ACVR2A WILD-TYPE         11         16       20         1
D11V10, multiclass

Clustering(12) Variable = TNFRSF10C MUTATION ANALYSIS
D12V1, survival
                     sevent
clus2                  0  1
  TNFRSF10C MUTATED    1  0
  TNFRSF10C WILD-TYPE 68 11
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  1                  79 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  0                  11 
$`TNFRSF10C MUTATED`
TCGA-AA-3844 
        0.92 

$`TNFRSF10C WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 
       15.52        10.92         9.14         8.09         1.02         0.99 
TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 
        0.99         1.02         2.01         0.99         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3846 
        0.99         0.99         0.99         1.02         1.02         0.99 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
        0.99         1.02         0.99         0.99         0.99         1.02 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 
        0.99         0.99         2.01         2.01         0.99         1.02 
TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        0.99        13.94        18.02        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.02        18.02        17.00         4.01        27.02        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.00        14.99        21.99        20.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        13.02        12.00        12.00        13.02        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       20.98        39.06        51.95        39.95         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 
        0.92        40.96        39.95        18.02        40.93        16.31 
TCGA-AY-4071 
        0.95 

  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
               0.92                0.92 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
               0.92               51.95 
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
               0.92               12.00 
[1] "0.9 - 0.9 (0.9)"   "0.9 - 52.0 (12.0)"
         TCGA-A6-2670          TCGA-A6-2672          TCGA-A6-2674 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-3810          TCGA-AA-3518          TCGA-AA-3526 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3562          TCGA-AA-3666 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3685          TCGA-AA-3710 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3818 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE"   "TNFRSF10C MUTATED" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3854 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3856          TCGA-AA-3877          TCGA-AA-3939 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3941          TCGA-AA-3947          TCGA-AA-3949 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3966          TCGA-AA-3975 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3977          TCGA-AA-3986          TCGA-AA-A004 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00L          TCGA-AA-A00N          TCGA-AA-A00O 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A00Z          TCGA-AA-A010 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A017          TCGA-AA-A01D          TCGA-AA-A01F 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01G          TCGA-AA-A01I          TCGA-AA-A01K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01P          TCGA-AA-A01Q          TCGA-AA-A01R 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01S          TCGA-AA-A01T          TCGA-AA-A01V 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01X          TCGA-AA-A01Z          TCGA-AA-A024 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02O          TCGA-AA-A02W 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2670          TCGA-A6-2672          TCGA-A6-2674 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-3810          TCGA-AA-3518          TCGA-AA-3526 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3562          TCGA-AA-3666 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3685          TCGA-AA-3710 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3818 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE"   "TNFRSF10C MUTATED" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3854 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3856          TCGA-AA-3877          TCGA-AA-3939 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3941          TCGA-AA-3947          TCGA-AA-3949 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3966          TCGA-AA-3975 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3977          TCGA-AA-3986          TCGA-AA-A004 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00L          TCGA-AA-A00N          TCGA-AA-A00O 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A00Z          TCGA-AA-A010 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A017          TCGA-AA-A01D          TCGA-AA-A01F 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01G          TCGA-AA-A01I          TCGA-AA-A01K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01P          TCGA-AA-A01Q          TCGA-AA-A01R 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01S          TCGA-AA-A01T          TCGA-AA-A01V 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01X          TCGA-AA-A01Z          TCGA-AA-A024 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02O          TCGA-AA-A02W 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2670          TCGA-A6-2672          TCGA-A6-2674 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-3810          TCGA-AA-3518          TCGA-AA-3526 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3562          TCGA-AA-3666 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3685          TCGA-AA-3710 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3818 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3844 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE"   "TNFRSF10C MUTATED" 
         TCGA-AA-3846          TCGA-AA-3848          TCGA-AA-3854 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3856          TCGA-AA-3877          TCGA-AA-3939 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3941          TCGA-AA-3947          TCGA-AA-3949 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3952          TCGA-AA-3966          TCGA-AA-3975 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3977          TCGA-AA-3986          TCGA-AA-A004 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00A          TCGA-AA-A00D          TCGA-AA-A00E 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00F          TCGA-AA-A00J          TCGA-AA-A00K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00L          TCGA-AA-A00N          TCGA-AA-A00O 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00Q          TCGA-AA-A00R          TCGA-AA-A00U 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00W          TCGA-AA-A00Z          TCGA-AA-A010 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A017          TCGA-AA-A01D          TCGA-AA-A01F 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01G          TCGA-AA-A01I          TCGA-AA-A01K 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01P          TCGA-AA-A01Q          TCGA-AA-A01R 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01S          TCGA-AA-A01T          TCGA-AA-A01V 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01X          TCGA-AA-A01Z          TCGA-AA-A024 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A029          TCGA-AA-A02F          TCGA-AA-A02H 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02J          TCGA-AA-A02O          TCGA-AA-A02W 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02Y          TCGA-AA-A03F          TCGA-AA-A03J 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AY-4070          TCGA-AY-4071 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
[1] "Remove cluster labels:" "TNFRSF10C MUTATED"     
clus
  TNFRSF10C MUTATED TNFRSF10C WILD-TYPE 
                  1                  79 
         TCGA-A6-2670          TCGA-A6-2672          TCGA-A6-2674 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2676          TCGA-A6-2677          TCGA-A6-2678 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-2683          TCGA-A6-3807          TCGA-A6-3808 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-A6-3810          TCGA-AA-3518          TCGA-AA-3526 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3555          TCGA-AA-3562          TCGA-AA-3666 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3679          TCGA-AA-3685          TCGA-AA-3710 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3715          TCGA-AA-3811          TCGA-AA-3818 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3837          TCGA-AA-3842          TCGA-AA-3846 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3848          TCGA-AA-3854          TCGA-AA-3856 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3877          TCGA-AA-3939          TCGA-AA-3941 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3947          TCGA-AA-3949          TCGA-AA-3952 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3966          TCGA-AA-3975          TCGA-AA-3977 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-3986          TCGA-AA-A004          TCGA-AA-A00A 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00D          TCGA-AA-A00E          TCGA-AA-A00F 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00J          TCGA-AA-A00K          TCGA-AA-A00L 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00N          TCGA-AA-A00O          TCGA-AA-A00Q 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00R          TCGA-AA-A00U          TCGA-AA-A00W 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A00Z          TCGA-AA-A010          TCGA-AA-A017 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01D          TCGA-AA-A01F          TCGA-AA-A01G 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01I          TCGA-AA-A01K          TCGA-AA-A01P 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01Q          TCGA-AA-A01R          TCGA-AA-A01S 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01T          TCGA-AA-A01V          TCGA-AA-A01X 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A01Z          TCGA-AA-A024          TCGA-AA-A029 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02F          TCGA-AA-A02H          TCGA-AA-A02J 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A02O          TCGA-AA-A02W          TCGA-AA-A02Y 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AA-A03F          TCGA-AA-A03J          TCGA-AY-4070 
"TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" "TNFRSF10C WILD-TYPE" 
         TCGA-AY-4071 
"TNFRSF10C WILD-TYPE" 
D12V2, continuous
D12V3, binary
                     cls
clus                   0  1
  TNFRSF10C MUTATED    2  4
  TNFRSF10C WILD-TYPE 75 74
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF10C MUTATED      2    4
  TNFRSF10C WILD-TYPE   75   74
        clus
vv       TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  FEMALE                 2                  75
  MALE                   4                  74
D12V4, binary
                     cls
clus                    0   1
  TNFRSF10C MUTATED     6   0
  TNFRSF10C WILD-TYPE 123  24
[1] "tbl2"
                     cls
clus                  [,1] [,2]
  TNFRSF10C MUTATED      6    0
  TNFRSF10C WILD-TYPE  123   24
                               clus
vv                              TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  COLON ADENOCARCINOMA                          6                 123
  COLON MUCINOUS ADENOCARCINOMA                 0                  24
                     vv
clus                   M0  M1 M1A
  TNFRSF10C MUTATED     3   3   0
  TNFRSF10C WILD-TYPE 128  18   1
D12V5, multiclass
     clus
vv    TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  M0                  3                 128
  M1                  3                  18
  M1A                 0                   1
                     vv
clus                  N0 N1 N1B N2 N2A
  TNFRSF10C MUTATED    2  1   0  3   0
  TNFRSF10C WILD-TYPE 89 28   1 30   1
D12V6, multiclass
                     vv
clus                   R0  R1  R2  RX
  TNFRSF10C MUTATED     3   0   3   0
  TNFRSF10C WILD-TYPE 126   1  16   1
D12V7, multiclass
    clus
vv   TNFRSF10C MUTATED TNFRSF10C WILD-TYPE
  R0                 3                 126
  R1                 0                   1
  R2                 3                  16
  RX                 0                   1
D12V8, continuous
D12V9, continuous
                     vv
clus                  STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  TNFRSF10C MUTATED         2        0         0         0         0          0
  TNFRSF10C WILD-TYPE      29       14        39         4        14          2
                     vv
clus                  STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  TNFRSF10C MUTATED            0          1        3         0
  TNFRSF10C WILD-TYPE         12         15       18         1
D12V10, multiclass

Clustering(13) Variable = SMAD2 MUTATION ANALYSIS
D13V1, survival
                 sevent
clus2              0  1
  SMAD2 MUTATED    4  2
  SMAD2 WILD-TYPE 65  9
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              6              74 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
              2               9 
$`SMAD2 MUTATED`
TCGA-AA-3842 TCGA-AA-3977 TCGA-AA-A00N TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 
        1.02         1.02         4.01        35.01        39.06        51.95 

$`SMAD2 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 
       15.52        10.92         9.14         8.09         1.02         0.99 
TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 
        0.99         1.02         2.01         0.99         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 
        0.99         0.99         0.99         1.02         0.92         0.99 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
        0.99         1.02         0.99         0.99         0.99         1.02 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3986 
        0.99         0.99         2.01         2.01         0.99         0.99 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        18.02        19.00        30.02        34.03        18.02 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.02        17.00        27.02        27.02         0.99        17.00 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        20.98        15.02         0.99        13.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        12.00        13.02        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        26.01        20.98        39.95         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        40.96        39.95        18.02        40.93 
TCGA-AY-4070 TCGA-AY-4071 
       16.31         0.95 

  SMAD2 MUTATED SMAD2 WILD-TYPE 
           1.02            0.92 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          51.95           40.96 
  SMAD2 MUTATED SMAD2 WILD-TYPE 
          19.51           11.46 
[1] "1.0 - 52.0 (19.5)" "0.9 - 41.0 (11.5)"
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
  "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "SMAD2 MUTATED"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
  "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "SMAD2 MUTATED"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
  "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"SMAD2 WILD-TYPE"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
  "SMAD2 MUTATED"   "SMAD2 MUTATED" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" "SMAD2 WILD-TYPE" 
[1] "hr=" "1.6"
D13V2, continuous
D13V3, binary
                 cls
clus               0  1
  SMAD2 MUTATED    3  7
  SMAD2 WILD-TYPE 74 71
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      3    7
  SMAD2 WILD-TYPE   74   71
        clus
vv       SMAD2 MUTATED SMAD2 WILD-TYPE
  FEMALE             3              74
  MALE               7              71
D13V4, binary
                 cls
clus                0   1
  SMAD2 MUTATED     7   3
  SMAD2 WILD-TYPE 122  21
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SMAD2 MUTATED      7    3
  SMAD2 WILD-TYPE  122   21
                               clus
vv                              SMAD2 MUTATED SMAD2 WILD-TYPE
  COLON ADENOCARCINOMA                      7             122
  COLON MUCINOUS ADENOCARCINOMA             3              21
                 vv
clus               M0  M1 M1A
  SMAD2 MUTATED     7   2   0
  SMAD2 WILD-TYPE 124  19   1
D13V5, multiclass
     clus
vv    SMAD2 MUTATED SMAD2 WILD-TYPE
  M0              7             124
  M1              2              19
  M1A             0               1
                 vv
clus              N0 N1 N1B N2 N2A
  SMAD2 MUTATED    7  2   0  1   0
  SMAD2 WILD-TYPE 84 27   1 32   1
D13V6, multiclass
                 vv
clus               R0  R1  R2  RX
  SMAD2 MUTATED     7   0   2   0
  SMAD2 WILD-TYPE 122   1  17   1
D13V7, multiclass
    clus
vv   SMAD2 MUTATED SMAD2 WILD-TYPE
  R0             7             122
  R1             0               1
  R2             2              17
  RX             0               1
D13V8, continuous
D13V9, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  SMAD2 MUTATED         1        4         0         1         0          1
  SMAD2 WILD-TYPE      30       10        39         3        14          1
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  SMAD2 MUTATED            0          0        2         0
  SMAD2 WILD-TYPE         12         16       19         1
D13V10, multiclass

Clustering(14) Variable = ACOT4 MUTATION ANALYSIS
D14V1, survival
                 sevent
clus2              0  1
  ACOT4 MUTATED    2  0
  ACOT4 WILD-TYPE 67 11
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              2              78 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              0              11 
$`ACOT4 MUTATED`
TCGA-AA-3877 TCGA-AA-3939 
        0.99         0.99 

$`ACOT4 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 
       15.52        10.92         9.14         8.09         1.02         0.99 
TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 
        0.99         1.02         2.01         0.99         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99         0.99         0.99         1.02         1.02         0.92 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 TCGA-AA-3947 
        0.99         0.99         1.02         0.99         1.02         0.99 
TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 
        0.99         2.01         2.01         0.99         1.02         0.99 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        18.02        19.00        30.02        34.03        18.02 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.02        17.00         4.01        27.02        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       17.00        14.99        21.99        20.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       13.02        12.00        12.00        13.02        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        20.98 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.95        39.95         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       40.96        39.95        18.02        40.93        16.31         0.95 

  ACOT4 MUTATED ACOT4 WILD-TYPE 
           0.99            0.92 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
           0.99           51.95 
  ACOT4 MUTATED ACOT4 WILD-TYPE 
           0.99           12.00 
[1] "1.0 - 1.0 (1.0)"   "0.9 - 52.0 (12.0)"
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
  "ACOT4 MUTATED"   "ACOT4 MUTATED" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
  "ACOT4 MUTATED"   "ACOT4 MUTATED" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
  "ACOT4 MUTATED"   "ACOT4 MUTATED" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
[1] "Remove cluster labels:" "ACOT4 MUTATED"         
clus
  ACOT4 MUTATED ACOT4 WILD-TYPE 
              2              78 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3941      TCGA-AA-3947      TCGA-AA-3949      TCGA-AA-3952 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-3966      TCGA-AA-3975      TCGA-AA-3977      TCGA-AA-3986 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D      TCGA-AA-A00E 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K      TCGA-AA-A00L 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q      TCGA-AA-A00R 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z      TCGA-AA-A010 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F      TCGA-AA-A01G 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01I      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A024      TCGA-AA-A029 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02O 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071 
"ACOT4 WILD-TYPE" "ACOT4 WILD-TYPE" 
D14V2, continuous
D14V3, binary
                 cls
clus               0  1
  ACOT4 MUTATED    1  2
  ACOT4 WILD-TYPE 76 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT4 MUTATED      1    2
  ACOT4 WILD-TYPE   76   76
        clus
vv       ACOT4 MUTATED ACOT4 WILD-TYPE
  FEMALE             1              76
  MALE               2              76
D14V4, binary
                 cls
clus                0   1
  ACOT4 MUTATED     2   1
  ACOT4 WILD-TYPE 127  23
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ACOT4 MUTATED      2    1
  ACOT4 WILD-TYPE  127   23
                               clus
vv                              ACOT4 MUTATED ACOT4 WILD-TYPE
  COLON ADENOCARCINOMA                      2             127
  COLON MUCINOUS ADENOCARCINOMA             1              23
                 vv
clus               M0  M1 M1A
  ACOT4 MUTATED     2   1   0
  ACOT4 WILD-TYPE 129  20   1
D14V5, multiclass
     clus
vv    ACOT4 MUTATED ACOT4 WILD-TYPE
  M0              2             129
  M1              1              20
  M1A             0               1
                 vv
clus              N0 N1 N1B N2 N2A
  ACOT4 MUTATED    2  0   0  1   0
  ACOT4 WILD-TYPE 89 29   1 32   1
D14V6, multiclass
                 vv
clus               R0  R1  R2  RX
  ACOT4 MUTATED     2   0   1   0
  ACOT4 WILD-TYPE 127   1  18   1
D14V7, multiclass
    clus
vv   ACOT4 MUTATED ACOT4 WILD-TYPE
  R0             2             127
  R1             0               1
  R2             1              18
  RX             0               1
D14V8, continuous
D14V9, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  ACOT4 MUTATED         1        0         1         0         0          0
  ACOT4 WILD-TYPE      30       14        38         4        14          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  ACOT4 MUTATED            0          0        1         0
  ACOT4 WILD-TYPE         12         16       20         1
D14V10, multiclass

Clustering(15) Variable = PCBP1 MUTATION ANALYSIS
D15V1, survival
                 sevent
clus2              0  1
  PCBP1 MUTATED    2  0
  PCBP1 WILD-TYPE 67 11
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              78 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              0              11 
$`PCBP1 MUTATED`
TCGA-AA-3941 TCGA-AA-A01I 
        1.02        12.00 

$`PCBP1 WILD-TYPE`
TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       13.91        16.54        17.19        14.70        17.79        14.37 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3808 TCGA-A6-3810 TCGA-AA-3518 TCGA-AA-3526 
       15.52        10.92         9.14         8.09         1.02         0.99 
TCGA-AA-3555 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3710 
        0.99         1.02         2.01         0.99         0.99         1.02 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
        0.99         0.99         0.99         1.02         1.02         0.92 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3877 TCGA-AA-3939 
        0.99         0.99         1.02         0.99         0.99         0.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3975 TCGA-AA-3977 
        0.99         0.99         2.01         2.01         0.99         1.02 
TCGA-AA-3986 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        0.99        13.94        18.02        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.02        18.02        17.00         4.01        27.02        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.00        14.99        21.99        20.98        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        13.02        12.00        13.02        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        20.98 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.95        39.95         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AY-4070 TCGA-AY-4071 
       40.96        39.95        18.02        40.93        16.31         0.95 

  PCBP1 MUTATED PCBP1 WILD-TYPE 
           1.02            0.92 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
          12.00           51.95 
  PCBP1 MUTATED PCBP1 WILD-TYPE 
           6.51           11.46 
[1] "1.0 - 12.0 (6.5)"  "0.9 - 52.0 (11.5)"
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3941      TCGA-AA-3947 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-3949      TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3977      TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00D      TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00K      TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Q      TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00Z      TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01F      TCGA-AA-A01G      TCGA-AA-A01I      TCGA-AA-A01K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE"   "PCBP1 MUTATED" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01P      TCGA-AA-A01Q      TCGA-AA-A01R      TCGA-AA-A01S 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01T      TCGA-AA-A01V      TCGA-AA-A01X      TCGA-AA-A01Z 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A024      TCGA-AA-A029      TCGA-AA-A02F      TCGA-AA-A02H 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02J      TCGA-AA-A02O      TCGA-AA-A02W      TCGA-AA-A02Y 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A03F      TCGA-AA-A03J      TCGA-AY-4070      TCGA-AY-4071 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
[1] "Remove cluster labels:" "PCBP1 MUTATED"         
clus
  PCBP1 MUTATED PCBP1 WILD-TYPE 
              2              78 
     TCGA-A6-2670      TCGA-A6-2672      TCGA-A6-2674      TCGA-A6-2676 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-2677      TCGA-A6-2678      TCGA-A6-2683      TCGA-A6-3807 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-A6-3808      TCGA-A6-3810      TCGA-AA-3518      TCGA-AA-3526 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3555      TCGA-AA-3562      TCGA-AA-3666      TCGA-AA-3679 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3685      TCGA-AA-3710      TCGA-AA-3715      TCGA-AA-3811 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3818      TCGA-AA-3837      TCGA-AA-3842      TCGA-AA-3844 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3846      TCGA-AA-3848      TCGA-AA-3854      TCGA-AA-3856 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3877      TCGA-AA-3939      TCGA-AA-3947      TCGA-AA-3949 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3952      TCGA-AA-3966      TCGA-AA-3975      TCGA-AA-3977 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-3986      TCGA-AA-A004      TCGA-AA-A00A      TCGA-AA-A00D 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00E      TCGA-AA-A00F      TCGA-AA-A00J      TCGA-AA-A00K 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00L      TCGA-AA-A00N      TCGA-AA-A00O      TCGA-AA-A00Q 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A00R      TCGA-AA-A00U      TCGA-AA-A00W      TCGA-AA-A00Z 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A010      TCGA-AA-A017      TCGA-AA-A01D      TCGA-AA-A01F 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01G      TCGA-AA-A01K      TCGA-AA-A01P      TCGA-AA-A01Q 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01R      TCGA-AA-A01S      TCGA-AA-A01T      TCGA-AA-A01V 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A01X      TCGA-AA-A01Z      TCGA-AA-A024      TCGA-AA-A029 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02F      TCGA-AA-A02H      TCGA-AA-A02J      TCGA-AA-A02O 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AA-A02W      TCGA-AA-A02Y      TCGA-AA-A03F      TCGA-AA-A03J 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
     TCGA-AY-4070      TCGA-AY-4071 
"PCBP1 WILD-TYPE" "PCBP1 WILD-TYPE" 
D15V2, continuous
D15V3, binary
                 cls
clus               0  1
  PCBP1 MUTATED    2  2
  PCBP1 WILD-TYPE 75 76
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      2    2
  PCBP1 WILD-TYPE   75   76
        clus
vv       PCBP1 MUTATED PCBP1 WILD-TYPE
  FEMALE             2              75
  MALE               2              76
D15V4, binary
                 cls
clus                0   1
  PCBP1 MUTATED     4   0
  PCBP1 WILD-TYPE 125  24
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCBP1 MUTATED      4    0
  PCBP1 WILD-TYPE  125   24
                               clus
vv                              PCBP1 MUTATED PCBP1 WILD-TYPE
  COLON ADENOCARCINOMA                      4             125
  COLON MUCINOUS ADENOCARCINOMA             0              24
                 vv
clus               M0  M1 M1A
  PCBP1 MUTATED     3   0   1
  PCBP1 WILD-TYPE 128  21   0
D15V5, multiclass
     clus
vv    PCBP1 MUTATED PCBP1 WILD-TYPE
  M0              3             128
  M1              0              21
  M1A             1               0
                 vv
clus              N0 N1 N1B N2 N2A
  PCBP1 MUTATED    3  0   1  0   0
  PCBP1 WILD-TYPE 88 29   0 33   1
D15V6, multiclass
                 vv
clus               R0  R1  R2  RX
  PCBP1 MUTATED     4   0   0   0
  PCBP1 WILD-TYPE 125   1  19   1
D15V7, multiclass
    clus
vv   PCBP1 MUTATED PCBP1 WILD-TYPE
  R0             4             125
  R1             0               1
  R2             0              19
  RX             0               1
D15V8, continuous
D15V9, continuous
                 vv
clus              STAGE I STAGE II STAGE IIA STAGE IIB STAGE III STAGE IIIA
  PCBP1 MUTATED         1        0         2         0         0          0
  PCBP1 WILD-TYPE      30       14        37         4        14          2
                 vv
clus              STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  PCBP1 MUTATED            0          0        0         1
  PCBP1 WILD-TYPE         12         16       21         0
D15V10, multiclass
                       V1.D                          V2 
            "Time to Death"                       "AGE" 
                         V3                          V4 
                   "GENDER"         "HISTOLOGICAL.TYPE" 
                         V5                          V6 
       "DISTANT.METASTASIS"     "LYMPH.NODE.METASTASIS" 
                         V7                          V8 
"COMPLETENESS.OF.RESECTION"     "NUMBER.OF.LYMPH.NODES" 
                         V9                         V10 
          "TUMOR.STAGECODE"     "NEOPLASM.DISEASESTAGE" 
> q(save="no")
