
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/480124/KIRP-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/KIRP-TP/4434786/KIRP-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=129, in cluster file=112, common to both=109
[1] "Reduce the number of clustering variables from 5 to 4."
[1]   4 109
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              4             105 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4             105 
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             4            105 
  IL32 MUTATED IL32 WILD-TYPE 
             4            105 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            7           102 
  NF2 MUTATED NF2 WILD-TYPE 
            7           102 
[1] "PPARGC1B MUTATION ANALYSIS"
[1] 3
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                106 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                106 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "KARNOFSKYPERFORMANCESCORE"             
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "YEAROFTOBACCOSMOKINGONSET"             
[19] "BATCHNUMBER"                           

Input Data has 19 rows and 109 columns.

[1] "Batch" "19"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
           1           27           NA            7           49          140 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-AL-3466 
           1            2           22            3           NA           NA 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1778         1636          922          763         1357          595 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
         498          307          347          334          147         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         856          803          626           14           33          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         196           36         2638          585           NA         1938 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
          NA           NA         1454           NA         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
         921          792          771          403           NA          232 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
          29          364           NA           84         3759           NA 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2948         2839           NA         1864         1532         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
         799          612           NA          232          213          217 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
         115          353          414         3950         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         418          114          445           92         2428         2459 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
          NA         1856         1669         1040          578          757 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
         208         1574         1479           NA         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         765          445          428         5924           NA          112 
TCGA-GL-8500 TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-IZ-8195 TCGA-IZ-8196 
         235           NA           NA           NA           33          123 
TCGA-J7-6720 
          NA 
Variable 1:'AGE':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=82,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'BATCH.NUMBER':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
[3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
[5] "PATHOLOGY.M.STAGE"           "GENDER"                     
[7] "KARNOFSKY.PERFORMANCE.SCORE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 109 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=42, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
61 13 34  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   61    13    35 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
61 13 34  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   61    13    35 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
22 11  4 
[1] "table(vv)"
vv
N0 N1 N2 
22 11  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
22 11  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
22 11  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = CDC27 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE 83 14
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              97 
  CDC27 MUTATED CDC27 WILD-TYPE 
              1              14 
$`CDC27 MUTATED`
TCGA-B9-5156 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-DW-5560 
        6.44         8.84        63.72        11.61 

$`CDC27 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8516 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
        0.72         0.10         9.63        58.45        53.79        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       25.08        44.61        19.56        16.37        10.09        11.41 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       10.98         4.83        50.50        28.14        26.40        20.58 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
        0.46         1.08        15.12         1.18        86.73        19.23 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
        3.78        13.61       129.86        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-IZ-8195 
       14.63        14.07       194.76         3.68         7.73         1.08 
TCGA-IZ-8196 
        4.04 

  CDC27 MUTATED CDC27 WILD-TYPE 
           6.44            0.03 
  CDC27 MUTATED CDC27 WILD-TYPE 
          63.72          194.76 
  CDC27 MUTATED CDC27 WILD-TYPE 
         10.225          19.000 
[1] "6.4 - 63.7 (10.2)"  "0.0 - 194.8 (19.0)"
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7996      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-8516      TCGA-A4-8518      TCGA-AL-3466      TCGA-AL-3467 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-AL-3468      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B3-4104      TCGA-B3-8121      TCGA-B9-4113      TCGA-B9-4114 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4115      TCGA-B9-4116      TCGA-B9-4117      TCGA-B9-4617 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-5155      TCGA-B9-5156      TCGA-B9-7268      TCGA-BQ-5875 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5876      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"CDC27 WILD-TYPE"   "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5881      TCGA-BQ-5882      TCGA-BQ-5883 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5884      TCGA-BQ-5885      TCGA-BQ-5886      TCGA-BQ-5887 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7044 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7046      TCGA-BQ-7048      TCGA-BQ-7049 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7053      TCGA-BQ-7055 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7056      TCGA-BQ-7058      TCGA-BQ-7059      TCGA-BQ-7060 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7061      TCGA-BQ-7062      TCGA-DW-5560      TCGA-DW-5561 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-DZ-6131 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6132      TCGA-DZ-6133      TCGA-DZ-6134      TCGA-DZ-6135 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6789 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-8500      TCGA-IZ-8195 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IZ-8196 
"CDC27 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7996      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-8516      TCGA-A4-8518      TCGA-AL-3466      TCGA-AL-3467 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-AL-3468      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B3-4104      TCGA-B3-8121      TCGA-B9-4113      TCGA-B9-4114 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4115      TCGA-B9-4116      TCGA-B9-4117      TCGA-B9-4617 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-5155      TCGA-B9-5156      TCGA-B9-7268      TCGA-BQ-5875 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5876      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"CDC27 WILD-TYPE"   "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5881      TCGA-BQ-5882      TCGA-BQ-5883 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5884      TCGA-BQ-5885      TCGA-BQ-5886      TCGA-BQ-5887 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7044 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7046      TCGA-BQ-7048      TCGA-BQ-7049 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7053      TCGA-BQ-7055 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7056      TCGA-BQ-7058      TCGA-BQ-7059      TCGA-BQ-7060 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7061      TCGA-BQ-7062      TCGA-DW-5560      TCGA-DW-5561 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-DZ-6131 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6132      TCGA-DZ-6133      TCGA-DZ-6134      TCGA-DZ-6135 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6789 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-8500      TCGA-IZ-8195 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IZ-8196 
"CDC27 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-7996      TCGA-A4-8098      TCGA-A4-8310      TCGA-A4-8311 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-A4-8516      TCGA-A4-8518      TCGA-AL-3466      TCGA-AL-3467 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-AL-3468      TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B1-5398      TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B3-4104      TCGA-B3-8121      TCGA-B9-4113      TCGA-B9-4114 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4115      TCGA-B9-4116      TCGA-B9-4117      TCGA-B9-4617 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-5155      TCGA-B9-5156      TCGA-B9-7268      TCGA-BQ-5875 
"CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5876      TCGA-BQ-5877      TCGA-BQ-5878      TCGA-BQ-5879 
"CDC27 WILD-TYPE"   "CDC27 MUTATED"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-BQ-5880      TCGA-BQ-5881      TCGA-BQ-5882      TCGA-BQ-5883 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5884      TCGA-BQ-5885      TCGA-BQ-5886      TCGA-BQ-5887 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890      TCGA-BQ-5891 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894      TCGA-BQ-7044 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7046      TCGA-BQ-7048      TCGA-BQ-7049 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7050      TCGA-BQ-7051      TCGA-BQ-7053      TCGA-BQ-7055 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7056      TCGA-BQ-7058      TCGA-BQ-7059      TCGA-BQ-7060 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7061      TCGA-BQ-7062      TCGA-DW-5560      TCGA-DW-5561 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" "CDC27 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-DZ-6131 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6132      TCGA-DZ-6133      TCGA-DZ-6134      TCGA-DZ-6135 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6789 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6790      TCGA-G7-6792      TCGA-G7-6793      TCGA-G7-6795 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-GL-6846      TCGA-GL-7966      TCGA-GL-8500      TCGA-IZ-8195 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-IZ-8196 
"CDC27 WILD-TYPE" 
[1] "hr=" "1.7"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  CDC27 MUTATED         1        0         1        1
  CDC27 WILD-TYPE      55        8        25        8
D1V3, multiclass
           clus
vv          CDC27 MUTATED CDC27 WILD-TYPE
  STAGE I               1              55
  STAGE II              0               8
  STAGE III             1              25
  STAGE IV              1               8
                 vv
clus              T1 T2 T3+T4
  CDC27 MUTATED    2  0     2
  CDC27 WILD-TYPE 59 13    33
D1V4, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                2              59
  T2                0              13
  T3+T4             2              33
                 vv
clus              N0 N1 N2
  CDC27 MUTATED    0  2  0
  CDC27 WILD-TYPE 22  9  4
D1V5, multiclass
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              35 
     TCGA-A4-7583      TCGA-A4-7585      TCGA-A4-7915      TCGA-AL-3466 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5885      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7051      TCGA-BQ-7056      TCGA-BQ-7058      TCGA-DZ-6131 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6789      TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-7501 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-GL-6846      TCGA-GL-7966      TCGA-J7-6720 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
                 vv
clus              M0 M1 MX
  CDC27 MUTATED    2  1  0
  CDC27 WILD-TYPE 52  4 42
D1V6, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  M0             2              52
  M1             1               4
  MX             0              42
D1V7, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  2
  CDC27 WILD-TYPE 32 73
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    2
  CDC27 WILD-TYPE   32   73
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             2              32
  MALE               2              73
D1V8, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1              20 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-AL-3466      TCGA-DW-5561 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838      TCGA-DW-7839 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842      TCGA-EV-5901 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5902      TCGA-EV-5903      TCGA-G7-6790      TCGA-G7-6793 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7501      TCGA-G7-7502 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 

Clustering(2) Variable = IL32 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2             0  1
  IL32 MUTATED    3  1
  IL32 WILD-TYPE 83 14
  IL32 MUTATED IL32 WILD-TYPE 
             4             97 
  IL32 MUTATED IL32 WILD-TYPE 
             1             14 
$`IL32 MUTATED`
TCGA-B3-3925 TCGA-B3-4103 TCGA-BQ-5893 TCGA-DW-7840 
       16.37        11.41         7.89         3.75 

$`IL32 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8516 TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
        0.72         0.10         9.63        58.45        53.79        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       25.08        44.61        19.56        10.09        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.14        26.40        20.58         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       15.12         6.44         1.18        86.73        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63         0.95        11.97         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.78        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       13.74        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        34.19        19.00        24.89         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.75        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-IZ-8195 
       14.63        14.07       194.76         3.68         7.73         1.08 
TCGA-IZ-8196 
        4.04 

  IL32 MUTATED IL32 WILD-TYPE 
          3.75           0.03 
  IL32 MUTATED IL32 WILD-TYPE 
         16.37         194.76 
  IL32 MUTATED IL32 WILD-TYPE 
          9.65          19.23 
[1] "3.8 - 16.4 (9.7)"   "0.0 - 194.8 (19.2)"
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7996     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8518     TCGA-AL-3466     TCGA-AL-3467 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-AL-3468     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-B3-4104     TCGA-B3-8121     TCGA-B9-4113     TCGA-B9-4114 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4116     TCGA-B9-4117     TCGA-B9-4617 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268     TCGA-BQ-5875 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882     TCGA-BQ-5883 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886     TCGA-BQ-5887 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131 
  "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6132     TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-8500     TCGA-IZ-8195 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-IZ-8196 
"IL32 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7996     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8518     TCGA-AL-3466     TCGA-AL-3467 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-AL-3468     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-B3-4104     TCGA-B3-8121     TCGA-B9-4113     TCGA-B9-4114 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4116     TCGA-B9-4117     TCGA-B9-4617 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268     TCGA-BQ-5875 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882     TCGA-BQ-5883 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886     TCGA-BQ-5887 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131 
  "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6132     TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-8500     TCGA-IZ-8195 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-IZ-8196 
"IL32 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-7996     TCGA-A4-8098     TCGA-A4-8310     TCGA-A4-8311 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-A4-8516     TCGA-A4-8518     TCGA-AL-3466     TCGA-AL-3467 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-AL-3468     TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B1-5398     TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-B3-4104     TCGA-B3-8121     TCGA-B9-4113     TCGA-B9-4114 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4115     TCGA-B9-4116     TCGA-B9-4117     TCGA-B9-4617 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-5155     TCGA-B9-5156     TCGA-B9-7268     TCGA-BQ-5875 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5876     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5881     TCGA-BQ-5882     TCGA-BQ-5883 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5884     TCGA-BQ-5885     TCGA-BQ-5886     TCGA-BQ-5887 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7044 
"IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7045     TCGA-BQ-7046     TCGA-BQ-7048     TCGA-BQ-7049 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7053     TCGA-BQ-7055 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7056     TCGA-BQ-7058     TCGA-BQ-7059     TCGA-BQ-7060 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7061     TCGA-BQ-7062     TCGA-DW-5560     TCGA-DW-5561 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-DZ-6131 
  "IL32 MUTATED" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6132     TCGA-DZ-6133     TCGA-DZ-6134     TCGA-DZ-6135 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5901     TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6789 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6790     TCGA-G7-6792     TCGA-G7-6793     TCGA-G7-6795 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-6846     TCGA-GL-7966     TCGA-GL-8500     TCGA-IZ-8195 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-IZ-8196 
"IL32 WILD-TYPE" 
[1] "hr=" "4.9"
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  IL32 MUTATED         2        0         1        1
  IL32 WILD-TYPE      54        8        25        8
D2V3, multiclass
           clus
vv          IL32 MUTATED IL32 WILD-TYPE
  STAGE I              2             54
  STAGE II             0              8
  STAGE III            1             25
  STAGE IV             1              8
                vv
clus             T1 T2 T3+T4
  IL32 MUTATED    2  0     2
  IL32 WILD-TYPE 59 13    33
D2V4, multiclass
       clus
vv      IL32 MUTATED IL32 WILD-TYPE
  T1               2             59
  T2               0             13
  T3+T4            2             33
                vv
clus             N0 N1 N2
  IL32 MUTATED    0  1  0
  IL32 WILD-TYPE 22 10  4
D2V5, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             36 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-AL-3466 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5880     TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5888     TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5892     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7050     TCGA-BQ-7051     TCGA-BQ-7056     TCGA-BQ-7058 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6131     TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-7501     TCGA-GL-6846     TCGA-GL-7966     TCGA-J7-6720 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
                vv
clus             M0 M1 MX
  IL32 MUTATED    2  1  1
  IL32 WILD-TYPE 52  4 41
D2V6, multiclass
    clus
vv   IL32 MUTATED IL32 WILD-TYPE
  M0            2             52
  M1            1              4
  MX            1             41
D2V7, binary
                cls
clus              0  1
  IL32 MUTATED    0  4
  IL32 WILD-TYPE 34 71
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL32 MUTATED      0    4
  IL32 WILD-TYPE   34   71
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  FEMALE            0             34
  MALE              4             71
D2V8, continuous
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             20 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-AL-3466     TCGA-DW-5560 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7839     TCGA-DW-7841     TCGA-DW-7842     TCGA-EV-5901 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7501     TCGA-G7-7502 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 

Clustering(3) Variable = NF2 MUTATION ANALYSIS
D3V1, survival
               sevent
clus2            0  1
  NF2 MUTATED    6  1
  NF2 WILD-TYPE 80 14
  NF2 MUTATED NF2 WILD-TYPE 
            7            94 
  NF2 MUTATED NF2 WILD-TYPE 
            1            14 
$`NF2 MUTATED`
TCGA-A4-8098 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 TCGA-EV-5902 TCGA-G7-6797 
        4.60        86.73         8.84         2.76        19.00        25.15 
TCGA-GL-7966 
        3.68 

$`NF2 WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8516 
        0.89         0.23         1.61         0.03         0.07         0.72 
TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
        0.10         9.63        58.45        53.79        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       44.61        19.56        16.37        10.09        11.41        10.98 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        4.83        50.50        28.14        26.40        20.58         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 TCGA-BQ-5878 
        1.08        15.12         6.44         1.18        19.23        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       61.02        54.87        34.19        24.89         4.01        51.75 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        39.25        34.82        14.63        14.07 
TCGA-GL-6846 TCGA-GL-8500 TCGA-IZ-8195 TCGA-IZ-8196 
      194.76         7.73         1.08         4.04 

  NF2 MUTATED NF2 WILD-TYPE 
         2.76          0.03 
  NF2 MUTATED NF2 WILD-TYPE 
        86.73        194.76 
  NF2 MUTATED NF2 WILD-TYPE 
         8.84         17.80 
[1] "2.8 - 86.7 (8.8)"   "0.0 - 194.8 (17.8)"
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-8500    TCGA-IZ-8195 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IZ-8196 
"NF2 WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-8500    TCGA-IZ-8195 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IZ-8196 
"NF2 WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-A4-8098 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-A4-8310    TCGA-A4-8311    TCGA-A4-8516    TCGA-A4-8518    TCGA-AL-3466 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B3-8121    TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4117    TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5875    TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
  "NF2 MUTATED" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5885    TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-7044    TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7058    TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5560    TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7839    TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6132    TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-EV-5902    TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792 
  "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7501 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-G7-7502    TCGA-GL-6846    TCGA-GL-7966    TCGA-GL-8500    TCGA-IZ-8195 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-IZ-8196 
"NF2 WILD-TYPE" 
[1] "hr=" "1.4"
D3V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  NF2 MUTATED         2        0         3        2
  NF2 WILD-TYPE      54        8        23        7
D3V3, multiclass
           clus
vv          NF2 MUTATED NF2 WILD-TYPE
  STAGE I             2            54
  STAGE II            0             8
  STAGE III           3            23
  STAGE IV            2             7
               vv
clus            T1 T2 T3+T4
  NF2 MUTATED    3  0     4
  NF2 WILD-TYPE 58 13    31
D3V4, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              3            58
  T2              0            13
  T3+T4           4            31
               vv
clus            N0 N1 N2
  NF2 MUTATED    0  3  0
  NF2 WILD-TYPE 22  8  4
D3V5, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           0            22
  N1           3             8
  N2           0             4
               vv
clus            M0 M1 MX
  NF2 MUTATED    2  2  3
  NF2 WILD-TYPE 52  3 39
D3V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  M0           2            52
  M1           2             3
  MX           3            39
D3V7, binary
               cls
clus             0  1
  NF2 MUTATED    2  5
  NF2 WILD-TYPE 32 70
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    5
  NF2 WILD-TYPE   32   70
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           2            32
  MALE             5            70
D3V8, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            19 
   TCGA-A4-7286    TCGA-A4-7828    TCGA-AL-3466    TCGA-DW-5560    TCGA-DW-5561 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839    TCGA-DW-7840 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7841    TCGA-DW-7842    TCGA-EV-5901    TCGA-EV-5903    TCGA-G7-6790 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6793    TCGA-G7-6796    TCGA-G7-7501    TCGA-G7-7502 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 

Clustering(4) Variable = PPARGC1B MUTATION ANALYSIS
D4V1, survival
                    sevent
clus2                 0  1
  PPARGC1B MUTATED    3  0
  PPARGC1B WILD-TYPE 83 15
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 3                 98 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 0                 15 
$`PPARGC1B MUTATED`
TCGA-A4-8516 TCGA-B3-4103 TCGA-B9-4117 
        0.72        11.41         0.46 

$`PPARGC1B WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23         1.61         4.60         0.03         0.07 
TCGA-A4-8518 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
        0.10         9.63        58.45        53.79        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       44.61        19.56        16.37        10.09        10.98         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.14        26.40        20.58         1.08        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 
        3.78        11.61        13.61       129.86        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        34.19        19.00        24.89 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.75        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       25.15        14.63        14.07       194.76         3.68         7.73 
TCGA-IZ-8195 TCGA-IZ-8196 
        1.08         4.04 

  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
              0.46               0.03 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             11.41             194.76 
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
             0.720             19.115 
[1] "0.5 - 11.4 (0.7)"   "0.0 - 194.8 (19.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8518         TCGA-AL-3466 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3472 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE"   "PPARGC1B MUTATED" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4113 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-8500 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8518         TCGA-AL-3466 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3472 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE"   "PPARGC1B MUTATED" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4113 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-8500 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8098         TCGA-A4-8310         TCGA-A4-8311 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8516         TCGA-A4-8518         TCGA-AL-3466 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3472 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE"   "PPARGC1B MUTATED" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4113 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "PPARGC1B MUTATED" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-8500 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
[1] "hr="     "3300000"
D4V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  PPARGC1B MUTATED         1        0         1        0
  PPARGC1B WILD-TYPE      55        8        25        9
D4V3, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 97 
        TCGA-A4-7287         TCGA-A4-7583         TCGA-A4-7584 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7828 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-8098 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8518 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8630         TCGA-AL-3466         TCGA-AL-3468 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4104 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4115 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-7268         TCGA-BQ-5875 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7837         TCGA-DW-7838 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-8500         TCGA-HE-7128         TCGA-HE-7129 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7130         TCGA-IZ-8195         TCGA-IZ-8196 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-J7-6720 
"PPARGC1B WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  PPARGC1B MUTATED    1  1     1
  PPARGC1B WILD-TYPE 60 12    34
D4V4, multiclass
       clus
vv      PPARGC1B MUTATED PPARGC1B WILD-TYPE
  T1                   1                 60
  T2                   1                 12
  T3+T4                1                 34
                    vv
clus                 N0 N1 N2
  PPARGC1B MUTATED    0  0  0
  PPARGC1B WILD-TYPE 22 11  4
D4V5, multiclass
                    vv
clus                 M0 M1 MX
  PPARGC1B MUTATED    1  0  1
  PPARGC1B WILD-TYPE 53  5 41
D4V6, multiclass
[1] "Remove cluster labels:" "PPARGC1B MUTATED"      
clus
  PPARGC1B MUTATED PPARGC1B WILD-TYPE 
                 2                 99 
        TCGA-A4-7287         TCGA-A4-7288         TCGA-A4-7583 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-8098         TCGA-A4-8310 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8518         TCGA-A4-8630 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4617 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5875         TCGA-BQ-5876 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-GL-8500 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
        TCGA-IZ-8195         TCGA-IZ-8196         TCGA-J7-6720 
"PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" "PPARGC1B WILD-TYPE" 
D4V7, binary
                    cls
clus                  0  1
  PPARGC1B MUTATED    1  2
  PPARGC1B WILD-TYPE 33 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  PPARGC1B MUTATED      1    2
  PPARGC1B WILD-TYPE   33   73
        clus
vv       PPARGC1B MUTATED PPARGC1B WILD-TYPE
  FEMALE                1                 33
  MALE                  2                 73
D4V8, continuous
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
      "NEOPLASM.DISEASESTAGE"           "PATHOLOGY.T.STAGE" 
                           V5                            V6 
          "PATHOLOGY.N.STAGE"           "PATHOLOGY.M.STAGE" 
                           V7                            V8 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
> q(save="no")
