
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/347491/CESC-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2587644/1.GDAC_clinicalDataPicker.Finished/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=40, in cluster file=39, common to both=21
[1] "Reduce the number of clustering variables from 13 to 7."
[1]  7 21
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4               17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4               17 
[1] "TMCC1 MUTATION ANALYSIS"
[1] 3
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              18 
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              18 
[1] "PRG4 MUTATION ANALYSIS"
[1] 3
  PRG4 MUTATED PRG4 WILD-TYPE 
             4             17 
  PRG4 MUTATED PRG4 WILD-TYPE 
             4             17 
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              17 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              17 
[1] "NFE2L2 MUTATION ANALYSIS"
[1] 3
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               17 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               17 
[1] "UGT3A2 MUTATION ANALYSIS"
[1] 3
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               18 
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               18 
[1] "PRB2 MUTATION ANALYSIS"
[1] 3
  PRB2 MUTATED PRB2 WILD-TYPE 
             3             18 
  PRB2 MUTATED PRB2 WILD-TYPE 
             3             18 
[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] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "DISTANT.METASTASIS"                    
[15] "LYMPH.NODE.METASTASIS"                 
[16] "NUMBER.OF.LYMPH.NODES"                 
[17] "TUMOR.STAGECODE"                       
[18] "BATCHNUMBER"                           

Input Data has 18 rows and 21 columns.

[1] "Batch" "18"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
        1505          925         5385           NA           NA         1616 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK 
          NA           NA           NA         2155         1289           NA 
TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A1OD TCGA-EA-A1QT 
          81         2127         2892          376         3096            8 
TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
         178           37           37 
Variable 1:'AGE':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=14,	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:'STOPPEDSMOKINGYEAR':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DISTANT.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'LYMPH.NODE.METASTASIS':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'TUMOR.STAGECODE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "TOBACCOSMOKINGHISTORYINDICATOR"        
[5] "DISTANT.METASTASIS"                    
[6] "LYMPH.NODE.METASTASIS"                 
[7] "NUMBER.OF.LYMPH.NODES"                 
[8] "TUMOR.STAGECODE"                       
[1] "TUMOR.?STAGE" "8"           
[1] "stage2"
vv
 T1B T1B1 T1B2 T2A1  T2B 
   3    9    2    1    3 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 21 columns, 1 survival variables, and 8 non-survival variables.
AGE, nv=16, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=7, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=3, 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    2  2
  PIK3CA WILD-TYPE 13  4
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4               17 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               2                4 
$`PIK3CA MUTATED`
TCGA-C5-A1M5 TCGA-C5-A1MK TCGA-DR-A0ZM TCGA-FU-A23K 
       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 
          22.405           36.760 
[1] "1.2 - 67.5 (22.4)"  "0.3 - 177.0 (36.8)"
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-FU-A23L 
"PIK3CA WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-FU-A23L 
"PIK3CA WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
  "PIK3CA MUTATED" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" "PIK3CA WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE" "PIK3CA WILD-TYPE"   "PIK3CA MUTATED" 
      TCGA-FU-A23L 
"PIK3CA WILD-TYPE" 
[1] "hr=" "2.5"
D1V2, continuous
D1V3, binary
                  cls
clus               0 1
  PIK3CA MUTATED   1 3
  PIK3CA WILD-TYPE 8 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    3
  PIK3CA WILD-TYPE    8    9
     clus
vv    PIK3CA MUTATED PIK3CA WILD-TYPE
  NO               1                8
  YES              3                9
D1V4, continuous
[1] "Remove cluster labels:" "PIK3CA MUTATED"        
clus
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               1                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, continuous
D1V6, binary
                  cls
clus                0  1
  PIK3CA MUTATED    2  1
  PIK3CA WILD-TYPE 11  4
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      2    1
  PIK3CA WILD-TYPE   11    4
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0              2               11
  MX              1                4
D1V7, binary
                  cls
clus               0 1
  PIK3CA MUTATED   1 2
  PIK3CA WILD-TYPE 9 6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1    2
  PIK3CA WILD-TYPE    9    6
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  N0              1                9
  N1              2                6
D1V8, continuous
D1V9, continuous

Clustering(2) Variable = TMCC1 MUTATION ANALYSIS
D2V1, survival
                 sevent
clus2              0  1
  TMCC1 MUTATED    3  0
  TMCC1 WILD-TYPE 12  6
  TMCC1 MUTATED TMCC1 WILD-TYPE 
              3              18 
  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-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41         5.46        67.46        53.13        35.61 
TCGA-C5-A1MK TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        2.43        40.93        70.85        42.38        36.76         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
       69.93        95.08         0.26         5.85         1.22         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 
        101.790          36.185 
[1] "12.4 - 177.0 (101.8)" "0.3 - 95.1 (36.2)"   
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23L 
"TMCC1 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23L 
"TMCC1 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE"   "TMCC1 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "TMCC1 MUTATED" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" "TMCC1 WILD-TYPE" 
     TCGA-FU-A23L 
"TMCC1 WILD-TYPE" 
[1] "hr="     "2.7e+08"
D2V2, continuous
D2V3, binary
                 cls
clus               0  1
  TMCC1 MUTATED    2  1
  TMCC1 WILD-TYPE  7 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE    7   11
     clus
vv    TMCC1 MUTATED TMCC1 WILD-TYPE
  NO              2               7
  YES             1              11
D2V4, continuous
D2V5, continuous
D2V6, binary
                 cls
clus               0  1
  TMCC1 MUTATED    2  1
  TMCC1 WILD-TYPE 11  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE   11    4
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  M0             2              11
  MX             1               4
D2V7, binary
                 cls
clus              0 1
  TMCC1 MUTATED   2 1
  TMCC1 WILD-TYPE 8 7
[1] "tbl2"
                 cls
clus              [,1] [,2]
  TMCC1 MUTATED      2    1
  TMCC1 WILD-TYPE    8    7
    clus
vv   TMCC1 MUTATED TMCC1 WILD-TYPE
  N0             2               8
  N1             1               7
D2V8, continuous
D2V9, continuous

Clustering(3) Variable = PRG4 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  PRG4 MUTATED    2  2
  PRG4 WILD-TYPE 13  4
  PRG4 MUTATED PRG4 WILD-TYPE 
             4             17 
  PRG4 MUTATED PRG4 WILD-TYPE 
             2              4 
$`PRG4 MUTATED`
TCGA-C5-A1BN TCGA-C5-A1MK TCGA-DS-A1OC TCGA-DS-A1OD 
        5.46         2.43        12.36       101.79 

$`PRG4 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1M5 TCGA-C5-A1MF TCGA-C5-A1MI 
       49.48        30.41       177.04        67.46        53.13        35.61 
TCGA-C5-A1MN TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       40.93        70.85        42.38        36.76         2.66        69.93 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
       95.08         0.26         5.85         1.22         1.22 

  PRG4 MUTATED PRG4 WILD-TYPE 
          2.43           0.26 
  PRG4 MUTATED PRG4 WILD-TYPE 
        101.79         177.04 
  PRG4 MUTATED PRG4 WILD-TYPE 
          8.91          40.93 
[1] "2.4 - 101.8 (8.9)"  "0.3 - 177.0 (40.9)"
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRG4 MUTATED" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-FU-A23L 
"PRG4 WILD-TYPE" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRG4 MUTATED" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-FU-A23L 
"PRG4 WILD-TYPE" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE"   "PRG4 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRG4 MUTATED" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-FU-A23L 
"PRG4 WILD-TYPE" 
[1] "hr=" "3.1"
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  PRG4 MUTATED    4  0
  PRG4 WILD-TYPE  5 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      4    0
  PRG4 WILD-TYPE    5   12
     clus
vv    PRG4 MUTATED PRG4 WILD-TYPE
  NO             4              5
  YES            0             12
D3V4, continuous
[1] "Remove cluster labels:" "PRG4 MUTATED"          
clus
  PRG4 MUTATED PRG4 WILD-TYPE 
             1              6 
    TCGA-BI-A0VR     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MN 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-DR-A0ZM     TCGA-EX-A1H5 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
D3V5, continuous
D3V6, binary
                cls
clus              0  1
  PRG4 MUTATED    2  0
  PRG4 WILD-TYPE 11  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      2    0
  PRG4 WILD-TYPE   11    5
    clus
vv   PRG4 MUTATED PRG4 WILD-TYPE
  M0            2             11
  MX            0              5
D3V7, binary
                cls
clus             0 1
  PRG4 MUTATED   1 1
  PRG4 WILD-TYPE 9 7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRG4 MUTATED      1    1
  PRG4 WILD-TYPE    9    7
    clus
vv   PRG4 MUTATED PRG4 WILD-TYPE
  N0            1              9
  N1            1              7
D3V8, continuous
[1] "Remove cluster labels:" "PRG4 MUTATED"          
clus
  PRG4 MUTATED PRG4 WILD-TYPE 
             2             16 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1M5 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-DR-A0ZL     TCGA-DR-A0ZM 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-DS-A0VK     TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
    TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K     TCGA-FU-A23L 
"PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" "PRG4 WILD-TYPE" 
D3V9, continuous

Clustering(4) Variable = CDC27 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    4  0
  CDC27 WILD-TYPE 11  6
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              17 
  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-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         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-A0VN TCGA-EA-A1QT TCGA-FU-A23K TCGA-FU-A23L 
        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          36.760 
[1] "5.8 - 101.8 (41.1)" "0.3 - 177.0 (36.8)"
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-FU-A23L 
"CDC27 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-FU-A23L 
"CDC27 WILD-TYPE" 
     TCGA-BI-A0VR      TCGA-BI-A0VS      TCGA-C5-A1BK      TCGA-C5-A1BN 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1M5      TCGA-C5-A1MF      TCGA-C5-A1MI      TCGA-C5-A1MK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZL      TCGA-DR-A0ZM      TCGA-DS-A0VK 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DS-A0VL      TCGA-DS-A0VM      TCGA-DS-A0VN      TCGA-DS-A1OC 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-DS-A1OD      TCGA-EA-A1QT      TCGA-EX-A1H5      TCGA-FU-A23K 
  "CDC27 MUTATED" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-FU-A23L 
"CDC27 WILD-TYPE" 
[1] "hr="     "2.8e+08"
D4V2, continuous
D4V3, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE  6 11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    1
  CDC27 WILD-TYPE    6   11
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  NO              3               6
  YES             1              11
D4V4, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1               6 
     TCGA-BI-A0VR      TCGA-C5-A1BN      TCGA-C5-A1MF      TCGA-C5-A1MI 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-C5-A1MN      TCGA-DR-A0ZM 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
D4V5, continuous
D4V6, binary
                 cls
clus               0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE 10  4
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      3    1
  CDC27 WILD-TYPE   10    4
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  M0             3              10
  MX             1               4
D4V7, binary
                 cls
clus              0 1
  CDC27 MUTATED   1 3
  CDC27 WILD-TYPE 9 5
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      1    3
  CDC27 WILD-TYPE    9    5
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  N0             1               9
  N1             3               5
D4V8, continuous
D4V9, continuous

Clustering(5) Variable = NFE2L2 MUTATION ANALYSIS
D5V1, survival
                  sevent
clus2               0  1
  NFE2L2 MUTATED    2  2
  NFE2L2 WILD-TYPE 13  4
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               4               17 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2                4 
$`NFE2L2 MUTATED`
TCGA-C5-A1MN TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       40.93        42.38        36.76        69.93 

$`NFE2L2 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         5.46        67.46        53.13 
TCGA-C5-A1MI TCGA-C5-A1MK TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A1OC 
       35.61         2.43        70.85         2.66        95.08        12.36 
TCGA-DS-A1OD TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
      101.79         0.26         5.85         1.22         1.22 

  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           36.76             0.26 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
           69.93           177.04 
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
          41.655           30.410 
[1] "36.8 - 69.9 (41.7)" "0.3 - 177.0 (30.4)"
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
  "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED"   "NFE2L2 MUTATED" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"NFE2L2 WILD-TYPE"   "NFE2L2 MUTATED" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-FU-A23L 
"NFE2L2 WILD-TYPE" 
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
                  cls
clus               0 1
  NFE2L2 MUTATED   1 3
  NFE2L2 WILD-TYPE 8 9
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      1    3
  NFE2L2 WILD-TYPE    8    9
     clus
vv    NFE2L2 MUTATED NFE2L2 WILD-TYPE
  NO               1                8
  YES              3                9
D5V4, continuous
[1] "Remove cluster labels:" "NFE2L2 MUTATED"        
clus
  NFE2L2 MUTATED NFE2L2 WILD-TYPE 
               2                5 
      TCGA-BI-A0VR       TCGA-C5-A1BN       TCGA-C5-A1MF       TCGA-C5-A1MI 
"NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" "NFE2L2 WILD-TYPE" 
      TCGA-EX-A1H5 
"NFE2L2 WILD-TYPE" 
D5V5, continuous
D5V6, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    3  0
  NFE2L2 WILD-TYPE 10  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      3    0
  NFE2L2 WILD-TYPE   10    5
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  M0              3               10
  MX              0                5
D5V7, binary
                  cls
clus                0  1
  NFE2L2 MUTATED    0  3
  NFE2L2 WILD-TYPE 10  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  NFE2L2 MUTATED      0    3
  NFE2L2 WILD-TYPE   10    5
    clus
vv   NFE2L2 MUTATED NFE2L2 WILD-TYPE
  N0              0               10
  N1              3                5
D5V8, continuous
D5V9, continuous

Clustering(6) Variable = UGT3A2 MUTATION ANALYSIS
D6V1, survival
                  sevent
clus2               0  1
  UGT3A2 MUTATED    3  0
  UGT3A2 WILD-TYPE 12  6
  UGT3A2 MUTATED UGT3A2 WILD-TYPE 
               3               18 
  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-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         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-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        2.66        95.08         0.26         5.85         1.22         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 
          69.930           36.185 
[1] "12.4 - 101.8 (69.9)" "0.3 - 177.0 (36.2)" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
  "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
  "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" 
      TCGA-BI-A0VR       TCGA-BI-A0VS       TCGA-C5-A1BK       TCGA-C5-A1BN 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1M5       TCGA-C5-A1MF       TCGA-C5-A1MI       TCGA-C5-A1MK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-C5-A1MN       TCGA-DR-A0ZL       TCGA-DR-A0ZM       TCGA-DS-A0VK 
"UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-DS-A0VL       TCGA-DS-A0VM       TCGA-DS-A0VN       TCGA-DS-A1OC 
"UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE"   "UGT3A2 MUTATED" 
      TCGA-DS-A1OD       TCGA-EA-A1QT       TCGA-EX-A1H5       TCGA-FU-A23K 
  "UGT3A2 MUTATED" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" "UGT3A2 WILD-TYPE" 
      TCGA-FU-A23L 
"UGT3A2 WILD-TYPE" 
[1] "hr="     "2.7e+08"
D6V2, continuous
D6V3, binary
                  cls
clus                0  1
  UGT3A2 MUTATED    2  1
  UGT3A2 WILD-TYPE  7 11
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      2    1
  UGT3A2 WILD-TYPE    7   11
     clus
vv    UGT3A2 MUTATED UGT3A2 WILD-TYPE
  NO               2                7
  YES              1               11
D6V4, continuous
D6V5, continuous
D6V6, binary
                  cls
clus                0  1
  UGT3A2 MUTATED    3  0
  UGT3A2 WILD-TYPE 10  5
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      3    0
  UGT3A2 WILD-TYPE   10    5
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  M0              3               10
  MX              0                5
D6V7, binary
                  cls
clus               0 1
  UGT3A2 MUTATED   1 2
  UGT3A2 WILD-TYPE 9 6
[1] "tbl2"
                  cls
clus               [,1] [,2]
  UGT3A2 MUTATED      1    2
  UGT3A2 WILD-TYPE    9    6
    clus
vv   UGT3A2 MUTATED UGT3A2 WILD-TYPE
  N0              1                9
  N1              2                6
D6V8, continuous
D6V9, continuous

Clustering(7) Variable = PRB2 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  PRB2 MUTATED    3  0
  PRB2 WILD-TYPE 12  6
  PRB2 MUTATED PRB2 WILD-TYPE 
             3             18 
  PRB2 MUTATED PRB2 WILD-TYPE 
             0              6 
$`PRB2 MUTATED`
TCGA-DS-A0VN TCGA-DS-A1OC TCGA-DS-A1OD 
       95.08        12.36       101.79 

$`PRB2 WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-C5-A1BK TCGA-C5-A1BN TCGA-C5-A1M5 TCGA-C5-A1MF 
       49.48        30.41       177.04         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-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
        2.66        69.93         0.26         5.85         1.22         1.22 

  PRB2 MUTATED PRB2 WILD-TYPE 
         12.36           0.26 
  PRB2 MUTATED PRB2 WILD-TYPE 
        101.79         177.04 
  PRB2 MUTATED PRB2 WILD-TYPE 
        95.080         36.185 
[1] "12.4 - 101.8 (95.1)" "0.3 - 177.0 (36.2)" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED"   "PRB2 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FU-A23L 
"PRB2 WILD-TYPE" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED"   "PRB2 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FU-A23L 
"PRB2 WILD-TYPE" 
    TCGA-BI-A0VR     TCGA-BI-A0VS     TCGA-C5-A1BK     TCGA-C5-A1BN 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1M5     TCGA-C5-A1MF     TCGA-C5-A1MI     TCGA-C5-A1MK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-C5-A1MN     TCGA-DR-A0ZL     TCGA-DR-A0ZM     TCGA-DS-A0VK 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-DS-A0VL     TCGA-DS-A0VM     TCGA-DS-A0VN     TCGA-DS-A1OC 
"PRB2 WILD-TYPE" "PRB2 WILD-TYPE"   "PRB2 MUTATED"   "PRB2 MUTATED" 
    TCGA-DS-A1OD     TCGA-EA-A1QT     TCGA-EX-A1H5     TCGA-FU-A23K 
  "PRB2 MUTATED" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" "PRB2 WILD-TYPE" 
    TCGA-FU-A23L 
"PRB2 WILD-TYPE" 
[1] "hr="     "2.7e+08"
D7V2, continuous
D7V3, binary
                cls
clus              0  1
  PRB2 MUTATED    3  0
  PRB2 WILD-TYPE  6 12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      3    0
  PRB2 WILD-TYPE    6   12
     clus
vv    PRB2 MUTATED PRB2 WILD-TYPE
  NO             3              6
  YES            0             12
D7V4, continuous
D7V5, continuous
D7V6, binary
                cls
clus              0  1
  PRB2 MUTATED    3  0
  PRB2 WILD-TYPE 10  5
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      3    0
  PRB2 WILD-TYPE   10    5
    clus
vv   PRB2 MUTATED PRB2 WILD-TYPE
  M0            3             10
  MX            0              5
D7V7, binary
                cls
clus             0 1
  PRB2 MUTATED   2 1
  PRB2 WILD-TYPE 8 7
[1] "tbl2"
                cls
clus             [,1] [,2]
  PRB2 MUTATED      2    1
  PRB2 WILD-TYPE    8    7
    clus
vv   PRB2 MUTATED PRB2 WILD-TYPE
  N0            2              8
  N1            1              7
D7V8, continuous
D7V9, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
                                      V6 
                    "DISTANT.METASTASIS" 
                                      V7 
                 "LYMPH.NODE.METASTASIS" 
                                      V8 
                 "NUMBER.OF.LYMPH.NODES" 
                                      V9 
                       "TUMOR.STAGECODE" 
> q(save="no")
