
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/423468/CESC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/CESC-TP/3349247/CESC-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=50, in cluster file=39, common to both=22
[1] "Reduce the number of clustering variables from 7 to 4."
[1]  4 22
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5               17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5               17 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              19 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              19 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              18 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              18 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               19 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               19 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NUMBERPACKYEARSSMOKED"                 
[12] "DISTANT.METASTASIS"                    
[13] "LYMPH.NODE.METASTASIS"                 
[14] "NUMBER.OF.LYMPH.NODES"                 
[15] "TUMOR.STAGECODE"                       
[16] "NEOPLASM.DISEASESTAGE"                 
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 22 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
        1505          925         1112         5385           NA           NA 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM 
        1616           NA           NA           NA         2155         1289 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A1OD 
          NA           81         2127         2892          376         3096 
TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
           8          178           37           37 
Variable 1:'AGE':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=15,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGECODE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "DISTANT.METASTASIS"                    
[5] "LYMPH.NODE.METASTASIS"                 
[6] "NUMBER.OF.LYMPH.NODES"                 
[7] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 T1B T1B1 T1B2 T2A1  T2B 
   4    9    2    1    3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 22 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=17, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=7, binary=FALSE, numeric=TRUE
DISTANT.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=2, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=4, binary=FALSE, numeric=TRUE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE

Clustering(1) Variable = PIK3CA MUTATION ANALYSIS
D1V1, survival
                  sevent
clus2               0  1
  PIK3CA MUTATED    3  2
  PIK3CA WILD-TYPE 13  4
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               5               17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               2                4 
$`PIK3CA MUTATED`
TCGA-C5-A1BI TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-FU-A23K 
       36.56        67.46         2.43        42.38         1.22 

$`PIK3CA WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41       177.04         5.46        53.13        35.61 
TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       40.93        70.85        36.76         2.66        69.93        95.08 
TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23L 
       12.36       101.79         0.26         5.85         1.22 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            1.22             0.26 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           67.46           177.04 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           36.56            36.76 
[1] "1.2 - 67.5 (36.6)"  "0.3 - 177.0 (36.8)"
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
[1] "hr=" "2.1"
D1V2, continuous
D1V3, binary
                  cls
clus               0 1
  PIK3CA MUTATED   3 2
  PIK3CA WILD-TYPE 8 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3    2
  PIK3CA WILD-TYPE    8    9
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               3                8
  YES              2                9
D1V4, continuous
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               2                6 
      TCGA-BI-A0VR       TCGA-C5-A1BN       TCGA-C5-A1MF       TCGA-C5-A1MI 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-EX-A1H5 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
D1V5, binary
                  cls
clus                0  1
  PIK3CA MUTATED    3  1
  PIK3CA WILD-TYPE 11  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      3    1
  PIK3CA WILD-TYPE   11    4
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              3               11
  MX              1                4
D1V6, binary
                  cls
clus               0 1
  PIK3CA MUTATED   1 3
  PIK3CA WILD-TYPE 9 6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    3
  PIK3CA WILD-TYPE    9    6
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0              1                9
  N1              3                6
D1V7, continuous
D1V8, continuous

Clustering(2) Variable = TMCC1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  TMCC1 MUTATED    3  0
  TMCC1 WILD-TYPE 13  6
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              19 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              0               6 
$`TMCC1 MUTATED`
TCGA-C5-A1BK TCGA-DS-A1OC TCGA-DS-A1OD 
      177.04        12.36       101.79 

$`TMCC1 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41        36.56         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
       35.61         2.43        40.93        70.85        42.38        36.76 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K 
        2.66        69.93        95.08         0.26         5.85         1.22 
TCGA-FU-A23L 
        1.22 

  TMCC1 MUTATED TMCC1 WILD-TYPE 
          12.36            0.26 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
         177.04           95.08 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
         101.79           36.56 
[1] "12.4 - 177.0 (101.8)" "0.3 - 95.1 (36.6)"   
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "TMCC1 MUTATED"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "TMCC1 MUTATED"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "TMCC1 MUTATED"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
[1] "hr="     "2.7e+08"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  TMCC1 MUTATED    2  1
  TMCC1 WILD-TYPE  9 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE    9   10
     clus
vv    TMCC1 MUTATED TMCC1 WILD-TYPE
  NO              2               9
  YES             1              10
D2V4, continuous
D2V5, binary
                 cls
clus               0  1
  TMCC1 MUTATED    2  1
  TMCC1 WILD-TYPE 12  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE   12    4
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  M0             2              12
  MX             1               4
D2V6, binary
                 cls
clus              0 1
  TMCC1 MUTATED   2 1
  TMCC1 WILD-TYPE 8 8
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE    8    8
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  N0             2               8
  N1             1               8
D2V7, continuous
D2V8, continuous

Clustering(3) Variable = CDC27 MUTATION ANALYSIS
D3V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    4  0
  CDC27 WILD-TYPE 12  6
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              18 
  CDC27 MUTATED CDC27 WILD-TYPE 
              0               6 
$`CDC27 MUTATED`
TCGA-DS-A0VM TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EX-A1H5 
       69.93        12.36       101.79         5.85 

$`CDC27 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM 
       53.13        35.61         2.43        40.93        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A23K TCGA-FU-A23L 
       36.76         2.66        95.08         0.26         1.22         1.22 

  CDC27 MUTATED CDC27 WILD-TYPE 
           5.85            0.26 
  CDC27 MUTATED CDC27 WILD-TYPE 
         101.79          177.04 
  CDC27 MUTATED CDC27 WILD-TYPE 
         41.145          36.660 
[1] "5.8 - 101.8 (41.1)" "0.3 - 177.0 (36.7)"
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BI      TCGA-C5-A1BK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1BN      TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MK      TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VK      TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DS-A1OC      TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5 
  "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-FU-A23K      TCGA-FU-A23L 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
[1] "hr="     "2.8e+08"
D3V2, continuous
D3V3, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE  8 10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    1
  CDC27 WILD-TYPE    8   10
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              3               8
  YES             1              10
D3V4, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1               7 
     TCGA-BI-A0VR      TCGA-C5-A1BI      TCGA-C5-A1BN      TCGA-C5-A1MF 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MI      TCGA-C5-A1MN      TCGA-DR-A0ZM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
D3V5, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE 11  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    1
  CDC27 WILD-TYPE   11    4
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  M0             3              11
  MX             1               4
D3V6, binary
                 cls
clus              0 1
  CDC27 MUTATED   1 3
  CDC27 WILD-TYPE 9 6
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    3
  CDC27 WILD-TYPE    9    6
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  N0             1               9
  N1             3               6
D3V7, continuous
D3V8, continuous

Clustering(4) Variable = UGT3A2 MUTATION ANALYSIS
D4V1, survival
                  sevent
clus2               0  1
  UGT3A2 MUTATED    3  0
  UGT3A2 WILD-TYPE 13  6
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               19 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               0                6 
$`UGT3A2 MUTATED`
TCGA-DS-A0VM TCGA-DS-A1OC TCGA-DS-A1OD 
       69.93        12.36       101.79 

$`UGT3A2 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BI TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 
       49.48        30.41        36.56       177.04         5.46        67.46 
TCGA-C5-A1MF TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM 
       53.13        35.61         2.43        40.93        70.85        42.38 
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K 
       36.76         2.66        95.08         0.26         5.85         1.22 
TCGA-FU-A23L 
        1.22 

  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
           12.36             0.26 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
          101.79           177.04 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
           69.93            36.56 
[1] "12.4 - 101.8 (69.9)" "0.3 - 177.0 (36.6)" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
  "UGT3A2 MUTATED"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
  "UGT3A2 MUTATED"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BI       TCGA-C5-A1BK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1BN       TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MK       TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VK       TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A1OC       TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5 
  "UGT3A2 MUTATED"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23K       TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
[1] "hr="     "2.7e+08"
D4V2, continuous
D4V3, binary
                  cls
clus                0  1
  UGT3A2 MUTATED    2  1
  UGT3A2 WILD-TYPE  9 10
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      2    1
  UGT3A2 WILD-TYPE    9   10
     clus
vv    UGT3A2 MUTATED UGT3A2 WILD-TYPE
  NO               2                9
  YES              1               10
D4V4, continuous
D4V5, binary
                  cls
clus                0  1
  UGT3A2 MUTATED    3  0
  UGT3A2 WILD-TYPE 11  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      3    0
  UGT3A2 WILD-TYPE   11    5
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  M0              3               11
  MX              0                5
D4V6, binary
                  cls
clus               0 1
  UGT3A2 MUTATED   1 2
  UGT3A2 WILD-TYPE 9 7
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      1    2
  UGT3A2 WILD-TYPE    9    7
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  N0              1                9
  N1              2                7
D4V7, continuous
D4V8, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
                    "DISTANT.METASTASIS" 
                                      V6 
                 "LYMPH.NODE.METASTASIS" 
                                      V7 
                 "NUMBER.OF.LYMPH.NODES" 
                                      V8 
                       "TUMOR.STAGECODE" 
> q(save="no")
