
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/423571/READ-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/READ-TP/3352996/READ-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"  "-oT="
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=336, in cluster file=69, common to both=69
[1]  3 69
[1] "APC MUTATION ANALYSIS"
[1] 3
  APC MUTATED APC WILD-TYPE 
           57            12 
  APC MUTATED APC WILD-TYPE 
           57            12 
[1] "KRAS MUTATION ANALYSIS"
[1] 3
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
  KRAS MUTATED KRAS WILD-TYPE 
            38             31 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
  TP53 MUTATED TP53 WILD-TYPE 
            45             24 
[1] "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 69 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3574 
         482          323          412          387          316           NA 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
         365           NA           NA           31           31           61 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
          NA           31           31           NA           NA           NA 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 
          30           NA           NA           NA           30           NA 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
          NA           NA           NA          242           29           30 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
          NA           NA           31           28           NA           31 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
          30           30           31           NA           NA           NA 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
          NA           31           31           NA           31           31 
TCGA-AG-4015 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
          NA          637          423          183          789          700 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W 
         518          484          396           31          365         2130 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1946          334         1519           NA           NA         1884 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1246         1156         2192 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	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=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'COMPLETENESS.OF.RESECTION':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'TUMOR.STAGECODE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NEOPLASM.DISEASESTAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "HISTOLOGICAL.TYPE"         "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 
 5 14 47  3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 69 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=4, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=3, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=12, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=7, binary=FALSE, numeric=FALSE

Clustering(1) Variable = APC MUTATION ANALYSIS
D1V1, survival
               sevent
clus2            0  1
  APC MUTATED   36  3
  APC WILD-TYPE  7  0
  APC MUTATED APC WILD-TYPE 
           39             7 
  APC MUTATED APC WILD-TYPE 
            3             0 
$`APC MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3581 TCGA-AG-3583 
       10.62        13.55        12.72        10.39         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        1.02         1.02         0.99         0.99         7.96         0.95 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02         0.92         1.02         0.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 
        1.02         1.02         1.02         1.02        20.94        13.91 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W 
        6.02        17.03        15.91        13.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       63.98        10.98        49.94         1.94        38.93        61.94 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
       40.96        38.01        72.07 

$`APC WILD-TYPE`
TCGA-AF-2689 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y 
       15.85        12.00         1.02         1.02        25.94        23.01 
TCGA-AG-A016 
        1.02 

  APC MUTATED APC WILD-TYPE 
         0.92          1.02 
  APC MUTATED APC WILD-TYPE 
        72.07         25.94 
  APC MUTATED APC WILD-TYPE 
         7.96         12.00 
[1] "0.9 - 72.1 (8.0)"  "1.0 - 25.9 (12.0)"
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3575    TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3586 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3587    TCGA-AG-3599    TCGA-AG-3605    TCGA-AG-3726    TCGA-AG-3727 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3878    TCGA-AG-3883    TCGA-AG-3887    TCGA-AG-3892    TCGA-AG-3893 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3894    TCGA-AG-3896    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3575    TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3586 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3587    TCGA-AG-3599    TCGA-AG-3605    TCGA-AG-3726    TCGA-AG-3727 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3878    TCGA-AG-3883    TCGA-AG-3887    TCGA-AG-3892    TCGA-AG-3893 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3894    TCGA-AG-3896    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
   TCGA-AF-2689    TCGA-AF-2691    TCGA-AF-2692    TCGA-AF-3400    TCGA-AF-3913 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3575    TCGA-AG-3581    TCGA-AG-3582    TCGA-AG-3583    TCGA-AG-3586 
"APC WILD-TYPE"   "APC MUTATED" "APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3587    TCGA-AG-3599    TCGA-AG-3605    TCGA-AG-3726    TCGA-AG-3727 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3878    TCGA-AG-3883    TCGA-AG-3887    TCGA-AG-3892    TCGA-AG-3893 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-3894    TCGA-AG-3896    TCGA-AG-3999    TCGA-AG-4001    TCGA-AG-4007 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-4008    TCGA-AG-A002    TCGA-AG-A008    TCGA-AG-A00C    TCGA-AG-A00H 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A00Y    TCGA-AG-A011    TCGA-AG-A014    TCGA-AG-A015    TCGA-AG-A016 
"APC WILD-TYPE"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" "APC WILD-TYPE" 
   TCGA-AG-A01L    TCGA-AG-A01W    TCGA-AG-A01Y    TCGA-AG-A020    TCGA-AG-A025 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A026    TCGA-AG-A02G    TCGA-AG-A02N    TCGA-AG-A02X    TCGA-AG-A032 
  "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED"   "APC MUTATED" 
   TCGA-AG-A036 
  "APC MUTATED" 
[1] "hr="     "8.7e+07"
D1V2, continuous
D1V3, binary
               cls
clus             0  1
  APC MUTATED   25 32
  APC WILD-TYPE  5  7
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     25   32
  APC WILD-TYPE    5    7
        clus
vv       APC MUTATED APC WILD-TYPE
  FEMALE          25             5
  MALE            32             7
D1V4, binary
               cls
clus             0  1
  APC MUTATED   47  6
  APC WILD-TYPE 10  2
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     47    6
  APC WILD-TYPE   10    2
                                clus
vv                               APC MUTATED APC WILD-TYPE
  RECTAL ADENOCARCINOMA                   47            10
  RECTAL MUCINOUS ADENOCARCINOMA           6             2
D1V5, binary
               cls
clus             0  1
  APC MUTATED   50  7
  APC WILD-TYPE  9  3
[1] "tbl2"
               cls
clus            [,1] [,2]
  APC MUTATED     50    7
  APC WILD-TYPE    9    3
    clus
vv   APC MUTATED APC WILD-TYPE
  M0          50             9
  M1           7             3
               vv
clus            N0 N1 N1A N2
  APC MUTATED   36 11   1  9
  APC WILD-TYPE  7  2   0  3
D1V6, multiclass
     clus
vv    APC MUTATED APC WILD-TYPE
  N0           36             7
  N1           11             2
  N1A           1             0
  N2            9             3
               vv
clus            R0 R1 R2
  APC MUTATED   49  1  6
  APC WILD-TYPE 10  0  2
D1V7, multiclass
    clus
vv   APC MUTATED APC WILD-TYPE
  R0          49            10
  R1           1             0
  R2           6             2
D1V8, continuous
D1V9, continuous
               vv
clus            STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  APC MUTATED        18        4        14         4          7          3
  APC WILD-TYPE       0        2         5         0          1          1
               vv
clus            STAGE IV
  APC MUTATED          6
  APC WILD-TYPE        3
D1V10, multiclass

Clustering(2) Variable = KRAS MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  KRAS MUTATED   29  0
  KRAS WILD-TYPE 14  3
  KRAS MUTATED KRAS WILD-TYPE 
            29             17 
  KRAS MUTATED KRAS WILD-TYPE 
             0              3 
$`KRAS MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       15.85        10.62        13.55        12.00         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3878 
        1.02         0.99         0.99         7.96         0.95         0.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A008 
        0.92         1.02         1.02         1.02         1.02        13.91 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01W 
        6.02        25.94        23.01        15.91        13.02        70.03 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        49.94        61.94        40.96        38.01 

$`KRAS WILD-TYPE`
TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3883 TCGA-AG-3893 
       12.72        10.39         1.02         1.02         1.02         0.99 
TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 
        0.99         1.02         1.02        20.94        17.03         1.02 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A036 
       12.00        63.98         1.94        38.93        72.07 

  KRAS MUTATED KRAS WILD-TYPE 
          0.92           0.99 
  KRAS MUTATED KRAS WILD-TYPE 
         70.03          72.07 
  KRAS MUTATED KRAS WILD-TYPE 
         10.62           1.94 
[1] "0.9 - 70.0 (10.6)" "1.0 - 72.1 (1.9)" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
"KRAS WILD-TYPE"   "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "KRAS MUTATED"   "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "KRAS MUTATED"   "KRAS MUTATED" "KRAS WILD-TYPE" "KRAS WILD-TYPE" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "KRAS MUTATED" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
"KRAS WILD-TYPE" "KRAS WILD-TYPE"   "KRAS MUTATED"   "KRAS MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "KRAS MUTATED" "KRAS WILD-TYPE" 
[1] "hr="     "3.2e+09"
D2V2, continuous
D2V3, binary
                cls
clus              0  1
  KRAS MUTATED   19 19
  KRAS WILD-TYPE 11 20
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     19   19
  KRAS WILD-TYPE   11   20
        clus
vv       KRAS MUTATED KRAS WILD-TYPE
  FEMALE           19             11
  MALE             19             20
D2V4, binary
                cls
clus              0  1
  KRAS MUTATED   29  6
  KRAS WILD-TYPE 28  2
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     29    6
  KRAS WILD-TYPE   28    2
                                clus
vv                               KRAS MUTATED KRAS WILD-TYPE
  RECTAL ADENOCARCINOMA                    29             28
  RECTAL MUCINOUS ADENOCARCINOMA            6              2
D2V5, binary
                cls
clus              0  1
  KRAS MUTATED   34  4
  KRAS WILD-TYPE 25  6
[1] "tbl2"
                cls
clus             [,1] [,2]
  KRAS MUTATED     34    4
  KRAS WILD-TYPE   25    6
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  M0           34             25
  M1            4              6
                vv
clus             N0 N1 N1A N2
  KRAS MUTATED   25  7   0  6
  KRAS WILD-TYPE 18  6   1  6
D2V6, multiclass
     clus
vv    KRAS MUTATED KRAS WILD-TYPE
  N0            25             18
  N1             7              6
  N1A            0              1
  N2             6              6
                vv
clus             R0 R1 R2
  KRAS MUTATED   36  0  2
  KRAS WILD-TYPE 23  1  6
D2V7, multiclass
    clus
vv   KRAS MUTATED KRAS WILD-TYPE
  R0           36             23
  R1            0              1
  R2            2              6
D2V8, continuous
D2V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  KRAS MUTATED        13        3         9         3          4          2
  KRAS WILD-TYPE       5        3        10         1          4          2
                vv
clus             STAGE IV
  KRAS MUTATED          4
  KRAS WILD-TYPE        5
D2V10, multiclass

Clustering(3) Variable = TP53 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  TP53 MUTATED   27  2
  TP53 WILD-TYPE 16  1
  TP53 MUTATED TP53 WILD-TYPE 
            29             17 
  TP53 MUTATED TP53 WILD-TYPE 
             2              1 
$`TP53 MUTATED`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3581 
       15.85        10.62        12.72        10.39        12.00         1.02 
TCGA-AG-3587 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
        1.02         0.99         7.96         0.99         1.02         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02         1.02         1.02         6.02        23.01        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       15.91         1.02        12.00        70.03        63.98        10.98 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AG-A036 
        1.94        61.94        40.96        38.01        72.07 

$`TP53 WILD-TYPE`
TCGA-AF-2692 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3727 
       13.55         1.02         2.01         1.02         0.99         0.95 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
        0.99         1.02         0.92         1.02         0.99        20.94 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02G 
       13.91        25.94        13.02        49.94        38.93 

  TP53 MUTATED TP53 WILD-TYPE 
          0.99           0.92 
  TP53 MUTATED TP53 WILD-TYPE 
         72.07          49.94 
  TP53 MUTATED TP53 WILD-TYPE 
         10.62           1.02 
[1] "1.0 - 72.1 (10.6)" "0.9 - 49.9 (1.0)" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AF-2689     TCGA-AF-2691     TCGA-AF-2692     TCGA-AF-3400 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AF-3913     TCGA-AG-3575     TCGA-AG-3581     TCGA-AG-3582 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3583     TCGA-AG-3586     TCGA-AG-3587     TCGA-AG-3599 
"TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-3605     TCGA-AG-3726     TCGA-AG-3727     TCGA-AG-3878 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-3883     TCGA-AG-3887     TCGA-AG-3892     TCGA-AG-3893 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE"   "TP53 MUTATED" 
    TCGA-AG-3894     TCGA-AG-3896     TCGA-AG-3999     TCGA-AG-4001 
"TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-4007     TCGA-AG-4008     TCGA-AG-A002     TCGA-AG-A008 
  "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-AG-A00C     TCGA-AG-A00H     TCGA-AG-A00Y     TCGA-AG-A011 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A014     TCGA-AG-A015     TCGA-AG-A016     TCGA-AG-A01L 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A01W     TCGA-AG-A01Y     TCGA-AG-A020     TCGA-AG-A025 
  "TP53 MUTATED"   "TP53 MUTATED"   "TP53 MUTATED" "TP53 WILD-TYPE" 
    TCGA-AG-A026     TCGA-AG-A02G     TCGA-AG-A02N     TCGA-AG-A02X 
  "TP53 MUTATED" "TP53 WILD-TYPE"   "TP53 MUTATED"   "TP53 MUTATED" 
    TCGA-AG-A032     TCGA-AG-A036 
  "TP53 MUTATED"   "TP53 MUTATED" 
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  TP53 MUTATED   19 26
  TP53 WILD-TYPE 11 13
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     19   26
  TP53 WILD-TYPE   11   13
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE           19             11
  MALE             26             13
D3V4, binary
                cls
clus              0  1
  TP53 MUTATED   41  4
  TP53 WILD-TYPE 16  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     41    4
  TP53 WILD-TYPE   16    4
                                clus
vv                               TP53 MUTATED TP53 WILD-TYPE
  RECTAL ADENOCARCINOMA                    41             16
  RECTAL MUCINOUS ADENOCARCINOMA            4              4
D3V5, binary
                cls
clus              0  1
  TP53 MUTATED   39  6
  TP53 WILD-TYPE 20  4
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED     39    6
  TP53 WILD-TYPE   20    4
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0           39             20
  M1            6              4
                vv
clus             N0 N1 N1A N2
  TP53 MUTATED   27  9   1  8
  TP53 WILD-TYPE 16  4   0  4
D3V6, multiclass
     clus
vv    TP53 MUTATED TP53 WILD-TYPE
  N0            27             16
  N1             9              4
  N1A            1              0
  N2             8              4
                vv
clus             R0 R1 R2
  TP53 MUTATED   40  1  4
  TP53 WILD-TYPE 19  0  4
D3V7, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  R0           40             19
  R1            1              0
  R2            4              4
D3V8, continuous
D3V9, continuous
                vv
clus             STAGE I STAGE II STAGE IIA STAGE III STAGE IIIB STAGE IIIC
  TP53 MUTATED         9        5        13         2          7          3
  TP53 WILD-TYPE       9        1         6         2          1          1
                vv
clus             STAGE IV
  TP53 MUTATED          5
  TP53 WILD-TYPE        4
D3V10, 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")
