
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/347488/KIRP-TP.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/2587662/1.GDAC_clinicalDataPicker.Finished/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=103, in cluster file=100, common to both=98
[1]  7 98
[1] "CDC27 MUTATION ANALYSIS"
[1] 3
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              94 
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              94 
[1] "MET MUTATION ANALYSIS"
[1] 3
  MET MUTATED MET WILD-TYPE 
            7            91 
  MET MUTATED MET WILD-TYPE 
            7            91 
[1] "IL32 MUTATION ANALYSIS"
[1] 3
  IL32 MUTATED IL32 WILD-TYPE 
             4             94 
  IL32 MUTATED IL32 WILD-TYPE 
             4             94 
[1] "PCF11 MUTATION ANALYSIS"
[1] 3
  PCF11 MUTATED PCF11 WILD-TYPE 
              7              91 
  PCF11 MUTATED PCF11 WILD-TYPE 
              7              91 
[1] "SFRS2IP MUTATION ANALYSIS"
[1] 3
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5                93 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5                93 
[1] "NF2 MUTATION ANALYSIS"
[1] 3
  NF2 MUTATED NF2 WILD-TYPE 
            6            92 
  NF2 MUTATED NF2 WILD-TYPE 
            6            92 
[1] "LGI4 MUTATION ANALYSIS"
[1] 3
  LGI4 MUTATED LGI4 WILD-TYPE 
             4             94 
  LGI4 MUTATED LGI4 WILD-TYPE 
             4             94 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "STOPPEDSMOKINGYEAR"                    
[19] "TOBACCOSMOKINGHISTORYINDICATOR"        
[20] "YEAROFTOBACCOSMOKINGONSET"             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 98 columns.

[1] "Batch" "21"   
[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-AL-3466 
           1           27           NA            7           49          293 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
        1778         1636          922          763         1357          336 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
         109          125          179          135         1536           21 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         329           92           14           33           19          196 
TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
          36         2638          585          269         1938          697 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
        1313         1454          658         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
         792          771          403          329          232           29 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
         364          240           84         3759           NA         2948 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2839           NA         1864         1532         1516          799 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         612           NA          232          213          217          115 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         353          414         3950         1142          744          418 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
         114          445           92         2428         2459         1556 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
        1856         1669          471          178          160          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
         977         1257           NA          928         1059          387 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7128 TCGA-HE-7129 
         428         5558           NA          112           NA           NA 
TCGA-HE-7130 TCGA-J7-6720 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=81,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
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:'STOPPEDSMOKINGYEAR':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[7] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
49  6 23  9 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 98 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
54 12 31  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   54    12    32 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
54 12 31  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   54    12    32 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
20 11  4 
[1] "table(vv)"
vv
N0 N1 N2 
20 11  4 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 
20 11  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
20 11  4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 49   6  23   9 
[1] "table(vv)"
vv
  I  II III  IV 
 49   6  23   9 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 49   6  23   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 49   6  23   9 

Clustering(1) Variable = CDC27 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2              0  1
  CDC27 MUTATED    3  1
  CDC27 WILD-TYPE 74 13
  CDC27 MUTATED CDC27 WILD-TYPE 
              4              87 
  CDC27 MUTATED CDC27 WILD-TYPE 
              1              13 
$`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-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         9.63        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        5.88         4.44        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
        0.46         1.08         0.62         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        10.82         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        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

  CDC27 MUTATED CDC27 WILD-TYPE 
           6.44            0.03 
  CDC27 MUTATED CDC27 WILD-TYPE 
          63.72          182.73 
  CDC27 MUTATED CDC27 WILD-TYPE 
         10.225          14.630 
[1] "6.4 - 63.7 (10.2)"  "0.0 - 182.7 (14.6)"
     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-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"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-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5886      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-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "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-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"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-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5886      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-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "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-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"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-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE"   "CDC27 MUTATED" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5886      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-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
  "CDC27 MUTATED" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
[1] "hr=" "1.7"
D1V2, continuous
D1V3, binary
                 cls
clus               0  1
  CDC27 MUTATED    2  2
  CDC27 WILD-TYPE 29 65
[1] "tbl2"
                 cls
clus              [,1] [,2]
  CDC27 MUTATED      2    2
  CDC27 WILD-TYPE   29   65
        clus
vv       CDC27 MUTATED CDC27 WILD-TYPE
  FEMALE             2              29
  MALE               2              65
D1V4, continuous
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              1              19 
     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-G7-7502 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
                 vv
clus              T1 T2 T3+T4
  CDC27 MUTATED    2  0     2
  CDC27 WILD-TYPE 52 12    30
D1V5, multiclass
       clus
vv      CDC27 MUTATED CDC27 WILD-TYPE
  T1                2              52
  T2                0              12
  T3+T4             2              30
                 vv
clus              N0 N1 N2
  CDC27 MUTATED    0  2  0
  CDC27 WILD-TYPE 20  9  4
D1V6, multiclass
[1] "Remove cluster labels:" "CDC27 MUTATED"         
clus
  CDC27 MUTATED CDC27 WILD-TYPE 
              2              33 
     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-3473      TCGA-AL-7173      TCGA-B1-5398      TCGA-B9-7268 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5882      TCGA-BQ-5885 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889      TCGA-BQ-5890 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893      TCGA-BQ-5894 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7045      TCGA-BQ-7048      TCGA-BQ-7050      TCGA-BQ-7051 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-BQ-7056      TCGA-BQ-7058      TCGA-DZ-6131      TCGA-G7-6789 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-GL-6846      TCGA-GL-7966 
"CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" "CDC27 WILD-TYPE" 
     TCGA-J7-6720 
"CDC27 WILD-TYPE" 
                 vv
clus              M0 M1 MX
  CDC27 MUTATED    2  1  0
  CDC27 WILD-TYPE 51  4 31
D1V7, multiclass
    clus
vv   CDC27 MUTATED CDC27 WILD-TYPE
  M0             2              51
  M1             1               4
  MX             0              31
                 vv
clus               I II III IV
  CDC27 MUTATED    1  0   1  1
  CDC27 WILD-TYPE 48  6  22  8
D1V8, multiclass
     clus
vv    CDC27 MUTATED CDC27 WILD-TYPE
  I               1              48
  II              0               6
  III             1              22
  IV              1               8

Clustering(2) Variable = MET MUTATION ANALYSIS
D2V1, survival
               sevent
clus2            0  1
  MET MUTATED    6  1
  MET WILD-TYPE 71 13
  MET MUTATED MET WILD-TYPE 
            7            84 
  MET MUTATED MET WILD-TYPE 
            1            13 
$`MET MUTATED`
TCGA-A4-7734 TCGA-AL-3472 TCGA-AL-7173 TCGA-BQ-5882 TCGA-BQ-7059 TCGA-DZ-6132 
        0.89        30.31        44.61        21.63         7.63        80.84 
TCGA-DZ-6135 
       54.87 

$`MET 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-A4-7915 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3473 
        0.23         1.61         9.63        58.45        53.79        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 
       11.05         3.58         4.11         5.88         4.44        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
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-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.17        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       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-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       20.12        11.28         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
       14.63         3.02        79.82        51.16        61.02        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        5.85         5.26         6.84        32.12        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       30.51        34.82        12.72        14.07       182.73         3.68 

  MET MUTATED MET WILD-TYPE 
         0.89          0.03 
  MET MUTATED MET WILD-TYPE 
        80.84        182.73 
  MET MUTATED MET WILD-TYPE 
       30.310        13.675 
[1] "0.9 - 80.8 (30.3)"  "0.0 - 182.7 (13.7)"
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-AL-3466 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
  "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-GL-7966 
"MET WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-AL-3466 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
  "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-GL-7966 
"MET WILD-TYPE" 
   TCGA-A4-7286    TCGA-A4-7287    TCGA-A4-7288    TCGA-A4-7583    TCGA-A4-7585 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-A4-7732    TCGA-A4-7734    TCGA-A4-7915    TCGA-A4-7996    TCGA-AL-3466 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-AL-3467    TCGA-AL-3468    TCGA-AL-3472    TCGA-AL-3473    TCGA-AL-7173 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-B1-5398    TCGA-B3-3925    TCGA-B3-3926    TCGA-B3-4103    TCGA-B3-4104 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
  "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"MET WILD-TYPE" "MET WILD-TYPE"   "MET MUTATED" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-GL-7966 
"MET WILD-TYPE" 
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
               cls
clus             0  1
  MET MUTATED    2  5
  MET WILD-TYPE 29 62
[1] "tbl2"
               cls
clus            [,1] [,2]
  MET MUTATED      2    5
  MET WILD-TYPE   29   62
        clus
vv       MET MUTATED MET WILD-TYPE
  FEMALE           2            29
  MALE             5            62
D2V4, continuous
               vv
clus            T1 T2 T3+T4
  MET MUTATED    4  1     2
  MET WILD-TYPE 50 11    30
D2V5, multiclass
       clus
vv      MET MUTATED MET WILD-TYPE
  T1              4            50
  T2              1            11
  T3+T4           2            30
               vv
clus            N0 N1 N2
  MET MUTATED    1  0  1
  MET WILD-TYPE 19 11  3
D2V6, multiclass
[1] "Remove cluster labels:" "MET MUTATED"           
clus
  MET MUTATED MET WILD-TYPE 
            2            33 
   TCGA-A4-7583    TCGA-A4-7585    TCGA-A4-7915    TCGA-AL-3466    TCGA-AL-3473 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-B1-5398    TCGA-B9-7268    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5880    TCGA-BQ-5885    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-5890    TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7048    TCGA-BQ-7050    TCGA-BQ-7051    TCGA-BQ-7056 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-BQ-7058    TCGA-DZ-6131    TCGA-G7-6789    TCGA-G7-6793    TCGA-G7-6795 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
   TCGA-GL-6846    TCGA-GL-7966    TCGA-J7-6720 
"MET WILD-TYPE" "MET WILD-TYPE" "MET WILD-TYPE" 
               vv
clus            M0 M1 MX
  MET MUTATED    4  0  3
  MET WILD-TYPE 49  5 28
D2V7, multiclass
    clus
vv   MET MUTATED MET WILD-TYPE
  M0           4            49
  M1           0             5
  MX           3            28
               vv
clus             I II III IV
  MET MUTATED    4  0   1  1
  MET WILD-TYPE 45  6  22  8
D2V8, multiclass
     clus
vv    MET MUTATED MET WILD-TYPE
  I             4            45
  II            0             6
  III           1            22
  IV            1             8

Clustering(3) Variable = IL32 MUTATION ANALYSIS
D3V1, survival
                sevent
clus2             0  1
  IL32 MUTATED    3  1
  IL32 WILD-TYPE 74 13
  IL32 MUTATED IL32 WILD-TYPE 
             4             87 
  IL32 MUTATED IL32 WILD-TYPE 
             1             13 
$`IL32 MUTATED`
TCGA-B3-3925 TCGA-B3-4103 TCGA-BQ-5893 TCGA-DW-7840 
        3.58         5.88         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-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         9.63        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 
       30.31        25.08        44.61        11.05         4.11         4.44 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50         0.69        10.82         3.02         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.62         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        10.82 
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        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

  IL32 MUTATED IL32 WILD-TYPE 
          3.58           0.03 
  IL32 MUTATED IL32 WILD-TYPE 
          7.89         182.73 
  IL32 MUTATED IL32 WILD-TYPE 
         4.815         15.480 
[1] "3.6 - 7.9 (4.8)"    "0.0 - 182.7 (15.5)"
    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-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"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-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
  "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "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-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"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-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
  "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "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-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"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-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
  "IL32 MUTATED" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"IL32 WILD-TYPE" "IL32 WILD-TYPE"   "IL32 MUTATED" "IL32 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
[1] "hr=" NA   
D3V2, continuous
D3V3, binary
                cls
clus              0  1
  IL32 MUTATED    0  4
  IL32 WILD-TYPE 31 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  IL32 MUTATED      0    4
  IL32 WILD-TYPE   31   63
        clus
vv       IL32 MUTATED IL32 WILD-TYPE
  FEMALE            0             31
  MALE              4             63
D3V4, continuous
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             19 
    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-G7-7502 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
                vv
clus             T1 T2 T3+T4
  IL32 MUTATED    2  0     2
  IL32 WILD-TYPE 52 12    30
D3V5, multiclass
       clus
vv      IL32 MUTATED IL32 WILD-TYPE
  T1               2             52
  T2               0             12
  T3+T4            2             30
                vv
clus             N0 N1 N2
  IL32 MUTATED    0  1  0
  IL32 WILD-TYPE 20 10  4
D3V6, multiclass
[1] "Remove cluster labels:" "IL32 MUTATED"          
clus
  IL32 MUTATED IL32 WILD-TYPE 
             1             34 
    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-3473     TCGA-AL-7173     TCGA-B1-5398     TCGA-B9-7268 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7048     TCGA-BQ-7050 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-BQ-7051     TCGA-BQ-7056     TCGA-BQ-7058     TCGA-DZ-6131 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795     TCGA-GL-6846 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" "IL32 WILD-TYPE" 
    TCGA-GL-7966     TCGA-J7-6720 
"IL32 WILD-TYPE" "IL32 WILD-TYPE" 
                vv
clus             M0 M1 MX
  IL32 MUTATED    2  1  1
  IL32 WILD-TYPE 51  4 30
D3V7, multiclass
    clus
vv   IL32 MUTATED IL32 WILD-TYPE
  M0            2             51
  M1            1              4
  MX            1             30
                vv
clus              I II III IV
  IL32 MUTATED    2  0   1  1
  IL32 WILD-TYPE 47  6  22  8
D3V8, multiclass
     clus
vv    IL32 MUTATED IL32 WILD-TYPE
  I              2             47
  II             0              6
  III            1             22
  IV             1              8

Clustering(4) Variable = PCF11 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2              0  1
  PCF11 MUTATED    6  1
  PCF11 WILD-TYPE 71 13
  PCF11 MUTATED PCF11 WILD-TYPE 
              7              84 
  PCF11 MUTATED PCF11 WILD-TYPE 
              1              13 
$`PCF11 MUTATED`
TCGA-B1-5398 TCGA-B9-4617 TCGA-BQ-5876 TCGA-BQ-7050 TCGA-BQ-7058 TCGA-DZ-6134 
       11.05         1.08        19.23        61.28        11.28        61.02 
TCGA-EV-5903 
        5.26 

$`PCF11 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-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         9.63        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       30.31        25.08        44.61         3.58         4.11         5.88 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        4.44        50.50         0.69        10.82         3.02         0.46 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
        0.62         6.44         1.18        86.73         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        10.82         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-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       96.92        93.34        44.84        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       20.12         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
       14.63         3.02        79.82        80.84        51.16        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       15.48         5.85         6.84        32.12        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       30.51        34.82        12.72        14.07       182.73         3.68 

  PCF11 MUTATED PCF11 WILD-TYPE 
           1.08            0.03 
  PCF11 MUTATED PCF11 WILD-TYPE 
          61.28          182.73 
  PCF11 MUTATED PCF11 WILD-TYPE 
          11.28           14.35 
[1] "1.1 - 61.3 (11.3)"  "0.0 - 182.7 (14.4)"
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7996      TCGA-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5886      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7996      TCGA-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5886      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7286      TCGA-A4-7287      TCGA-A4-7288      TCGA-A4-7583 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7585      TCGA-A4-7732      TCGA-A4-7734      TCGA-A4-7915 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-A4-7996      TCGA-AL-3466      TCGA-AL-3467      TCGA-AL-3468 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-AL-3472      TCGA-AL-3473      TCGA-AL-7173      TCGA-B1-5398 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-B3-3925      TCGA-B3-3926      TCGA-B3-4103      TCGA-B3-4104 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4113      TCGA-B9-4114      TCGA-B9-4115      TCGA-B9-4116 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-4117      TCGA-B9-4617      TCGA-B9-5155      TCGA-B9-5156 
"PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-B9-7268      TCGA-BQ-5875      TCGA-BQ-5876      TCGA-BQ-5877 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-5878      TCGA-BQ-5879      TCGA-BQ-5880      TCGA-BQ-5881 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5882      TCGA-BQ-5883      TCGA-BQ-5884      TCGA-BQ-5885 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5886      TCGA-BQ-5887      TCGA-BQ-5888      TCGA-BQ-5889 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5890      TCGA-BQ-5891      TCGA-BQ-5892      TCGA-BQ-5893 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-5894      TCGA-BQ-7044      TCGA-BQ-7045      TCGA-BQ-7046 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-BQ-7048      TCGA-BQ-7049      TCGA-BQ-7050      TCGA-BQ-7051 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" "PCF11 WILD-TYPE" 
     TCGA-BQ-7053      TCGA-BQ-7055      TCGA-BQ-7056      TCGA-BQ-7058 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE"   "PCF11 MUTATED" 
     TCGA-BQ-7059      TCGA-BQ-7060      TCGA-BQ-7061      TCGA-BQ-7062 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-5560      TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7838      TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7842      TCGA-DZ-6131      TCGA-DZ-6132      TCGA-DZ-6133 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DZ-6134      TCGA-DZ-6135      TCGA-EV-5901      TCGA-EV-5902 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EV-5903      TCGA-G7-6789      TCGA-G7-6790      TCGA-G7-6792 
  "PCF11 MUTATED" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6793      TCGA-G7-6795      TCGA-G7-6796      TCGA-G7-6797 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-7502      TCGA-GL-6846      TCGA-GL-7966 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
[1] "hr=" "1.3"
D4V2, continuous
D4V3, binary
                 cls
clus               0  1
  PCF11 MUTATED    1  6
  PCF11 WILD-TYPE 30 61
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PCF11 MUTATED      1    6
  PCF11 WILD-TYPE   30   61
        clus
vv       PCF11 MUTATED PCF11 WILD-TYPE
  FEMALE             1              30
  MALE               6              61
D4V4, continuous
[1] "Remove cluster labels:" "PCF11 MUTATED"         
clus
  PCF11 MUTATED PCF11 WILD-TYPE 
              1              19 
     TCGA-A4-7286      TCGA-A4-7828      TCGA-AL-3466      TCGA-DW-5560 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-5561      TCGA-DW-7834      TCGA-DW-7837      TCGA-DW-7838 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-DW-7839      TCGA-DW-7840      TCGA-DW-7841      TCGA-DW-7842 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-EV-5901      TCGA-EV-5902      TCGA-G7-6790      TCGA-G7-6793 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
     TCGA-G7-6796      TCGA-G7-6797      TCGA-G7-7502 
"PCF11 WILD-TYPE" "PCF11 WILD-TYPE" "PCF11 WILD-TYPE" 
                 vv
clus              T1 T2 T3+T4
  PCF11 MUTATED    5  0     2
  PCF11 WILD-TYPE 49 12    30
D4V5, multiclass
       clus
vv      PCF11 MUTATED PCF11 WILD-TYPE
  T1                5              49
  T2                0              12
  T3+T4             2              30
                 vv
clus              N0 N1 N2
  PCF11 MUTATED    2  0  1
  PCF11 WILD-TYPE 18 11  3
D4V6, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  N0             2              18
  N1             0              11
  N2             1               3
                 vv
clus              M0 M1 MX
  PCF11 MUTATED    5  0  1
  PCF11 WILD-TYPE 48  5 30
D4V7, multiclass
    clus
vv   PCF11 MUTATED PCF11 WILD-TYPE
  M0             5              48
  M1             0               5
  MX             1              30
                 vv
clus               I II III IV
  PCF11 MUTATED    4  0   2  0
  PCF11 WILD-TYPE 45  6  21  9
D4V8, multiclass
     clus
vv    PCF11 MUTATED PCF11 WILD-TYPE
  I               4              45
  II              0               6
  III             2              21
  IV              0               9

Clustering(5) Variable = SFRS2IP MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  SFRS2IP MUTATED    4  1
  SFRS2IP WILD-TYPE 73 13
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                5                86 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                1                13 
$`SFRS2IP MUTATED`
TCGA-A4-7286 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-DW-5560 
        0.03        25.35        10.82         0.95        11.61 

$`SFRS2IP WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
        0.23         1.61         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        11.05         3.58         4.11         5.88 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        4.44        50.50         0.69        10.82         3.02         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
        1.08         0.62         6.44         1.18        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       40.83        26.04        30.28        26.04        13.25         7.63 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       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-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        15.48         5.85         5.26         6.84        32.12 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       41.33        11.05        30.51        34.82        12.72        14.07 
TCGA-GL-6846 TCGA-GL-7966 
      182.73         3.68 

  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
             0.03              0.03 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
            25.35            182.73 
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
           10.820            15.055 
[1] "0.0 - 25.4 (10.8)"  "0.0 - 182.7 (15.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7996        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7996        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-A4-7996        TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"SFRS2IP WILD-TYPE"   "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7837 
  "SFRS2IP MUTATED" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7966 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
[1] "hr=" "3.3"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  SFRS2IP MUTATED    2  3
  SFRS2IP WILD-TYPE 29 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  SFRS2IP MUTATED      2    3
  SFRS2IP WILD-TYPE   29   64
        clus
vv       SFRS2IP MUTATED SFRS2IP WILD-TYPE
  FEMALE               2                29
  MALE                 3                64
D5V4, continuous
[1] "Remove cluster labels:" "SFRS2IP MUTATED"       
clus
  SFRS2IP MUTATED SFRS2IP WILD-TYPE 
                2                18 
       TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5561        TCGA-DW-7834 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901        TCGA-EV-5902 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7502 
"SFRS2IP WILD-TYPE" "SFRS2IP WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  SFRS2IP MUTATED    1  0     4
  SFRS2IP WILD-TYPE 53 12    28
D5V5, multiclass
       clus
vv      SFRS2IP MUTATED SFRS2IP WILD-TYPE
  T1                  1                53
  T2                  0                12
  T3+T4               4                28
                   vv
clus                N0 N1 N2
  SFRS2IP MUTATED    2  1  0
  SFRS2IP WILD-TYPE 18 10  4
D5V6, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  N0               2                18
  N1               1                10
  N2               0                 4
                   vv
clus                M0 M1 MX
  SFRS2IP MUTATED    3  1  0
  SFRS2IP WILD-TYPE 50  4 31
D5V7, multiclass
    clus
vv   SFRS2IP MUTATED SFRS2IP WILD-TYPE
  M0               3                50
  M1               1                 4
  MX               0                31
                   vv
clus                 I II III IV
  SFRS2IP MUTATED    1  0   2  1
  SFRS2IP WILD-TYPE 48  6  21  8
D5V8, multiclass
     clus
vv    SFRS2IP MUTATED SFRS2IP WILD-TYPE
  I                 1                48
  II                0                 6
  III               2                21
  IV                1                 8

Clustering(6) Variable = NF2 MUTATION ANALYSIS
D6V1, survival
               sevent
clus2            0  1
  NF2 MUTATED    5  1
  NF2 WILD-TYPE 72 13
  NF2 MUTATED NF2 WILD-TYPE 
            6            85 
  NF2 MUTATED NF2 WILD-TYPE 
            1            13 
$`NF2 MUTATED`
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5894 TCGA-EV-5902 TCGA-G7-6797 TCGA-GL-7966 
       86.73         8.84         2.76         5.85        12.72         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-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         9.63        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        5.88         4.44        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 
        0.46         1.08         0.62         6.44         1.18        19.23 
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        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63         0.95        11.97         7.89       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-5903 TCGA-G7-6789 
       51.16        61.02        54.87        15.48         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
       32.12        41.33        11.05        30.51        34.82        14.07 
TCGA-GL-6846 
      182.73 

  NF2 MUTATED NF2 WILD-TYPE 
         2.76          0.03 
  NF2 MUTATED NF2 WILD-TYPE 
        86.73        182.73 
  NF2 MUTATED NF2 WILD-TYPE 
        7.345        15.480 
[1] "2.8 - 86.7 (7.3)"   "0.0 - 182.7 (15.5)"
   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-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-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-7966 
  "NF2 MUTATED" 
   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-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-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-7966 
  "NF2 MUTATED" 
   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-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-B9-4113    TCGA-B9-4114    TCGA-B9-4115    TCGA-B9-4116    TCGA-B9-4117 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-B9-4617    TCGA-B9-5155    TCGA-B9-5156    TCGA-B9-7268    TCGA-BQ-5875 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-BQ-5876    TCGA-BQ-5877    TCGA-BQ-5878    TCGA-BQ-5879    TCGA-BQ-5880 
"NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5881    TCGA-BQ-5882    TCGA-BQ-5883    TCGA-BQ-5884    TCGA-BQ-5885 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5886    TCGA-BQ-5887    TCGA-BQ-5888    TCGA-BQ-5889    TCGA-BQ-5890 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-5891    TCGA-BQ-5892    TCGA-BQ-5893    TCGA-BQ-5894    TCGA-BQ-7044 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" 
   TCGA-BQ-7045    TCGA-BQ-7046    TCGA-BQ-7048    TCGA-BQ-7049    TCGA-BQ-7050 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7051    TCGA-BQ-7053    TCGA-BQ-7055    TCGA-BQ-7056    TCGA-BQ-7058 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-BQ-7059    TCGA-BQ-7060    TCGA-BQ-7061    TCGA-BQ-7062    TCGA-DW-5560 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-5561    TCGA-DW-7834    TCGA-DW-7837    TCGA-DW-7838    TCGA-DW-7839 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DW-7840    TCGA-DW-7841    TCGA-DW-7842    TCGA-DZ-6131    TCGA-DZ-6132 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-DZ-6133    TCGA-DZ-6134    TCGA-DZ-6135    TCGA-EV-5901    TCGA-EV-5902 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" 
   TCGA-EV-5903    TCGA-G7-6789    TCGA-G7-6790    TCGA-G7-6792    TCGA-G7-6793 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-G7-6795    TCGA-G7-6796    TCGA-G7-6797    TCGA-G7-7502    TCGA-GL-6846 
"NF2 WILD-TYPE" "NF2 WILD-TYPE"   "NF2 MUTATED" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
   TCGA-GL-7966 
  "NF2 MUTATED" 
[1] "hr=" "1.7"
D6V2, continuous
D6V3, binary
               cls
clus             0  1
  NF2 MUTATED    2  4
  NF2 WILD-TYPE 29 63
[1] "tbl2"
               cls
clus            [,1] [,2]
  NF2 MUTATED      2    4
  NF2 WILD-TYPE   29   63
        clus
vv       NF2 MUTATED NF2 WILD-TYPE
  FEMALE           2            29
  MALE             4            63
D6V4, continuous
[1] "Remove cluster labels:" "NF2 MUTATED"           
clus
  NF2 MUTATED NF2 WILD-TYPE 
            2            18 
   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-G7-7502 
"NF2 WILD-TYPE" "NF2 WILD-TYPE" "NF2 WILD-TYPE" 
               vv
clus            T1 T2 T3+T4
  NF2 MUTATED    2  0     4
  NF2 WILD-TYPE 52 12    28
D6V5, multiclass
       clus
vv      NF2 MUTATED NF2 WILD-TYPE
  T1              2            52
  T2              0            12
  T3+T4           4            28
               vv
clus            N0 N1 N2
  NF2 MUTATED    0  3  0
  NF2 WILD-TYPE 20  8  4
D6V6, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  N0           0            20
  N1           3             8
  N2           0             4
               vv
clus            M0 M1 MX
  NF2 MUTATED    2  2  2
  NF2 WILD-TYPE 51  3 29
D6V7, multiclass
    clus
vv   NF2 MUTATED NF2 WILD-TYPE
  M0           2            51
  M1           2             3
  MX           2            29
               vv
clus             I II III IV
  NF2 MUTATED    1  0   3  2
  NF2 WILD-TYPE 48  6  20  7
D6V8, multiclass
     clus
vv    NF2 MUTATED NF2 WILD-TYPE
  I             1            48
  II            0             6
  III           3            20
  IV            2             7

Clustering(7) Variable = LGI4 MUTATION ANALYSIS
D7V1, survival
                sevent
clus2             0  1
  LGI4 MUTATED    4  0
  LGI4 WILD-TYPE 73 14
  LGI4 MUTATED LGI4 WILD-TYPE 
             4             87 
  LGI4 MUTATED LGI4 WILD-TYPE 
             0             14 
$`LGI4 MUTATED`
TCGA-BQ-7048 TCGA-DW-5561 TCGA-DZ-6132 TCGA-GL-6846 
       93.34        13.61        80.84       182.73 

$`LGI4 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-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         9.63        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        5.88         4.44        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.58        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.37        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 
        7.00         7.13         3.78        11.61       129.86        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       24.46        13.74         3.75        14.63         3.02        79.82 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        6.84        32.12        41.33        11.05        30.51        34.82 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-7966 
       12.72        14.07         3.68 

  LGI4 MUTATED LGI4 WILD-TYPE 
         13.61           0.03 
  LGI4 MUTATED LGI4 WILD-TYPE 
        182.73         129.86 
  LGI4 MUTATED LGI4 WILD-TYPE 
         87.09          13.74 
[1] "13.6 - 182.7 (87.1)" "0.0 - 129.9 (13.7)" 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7996     TCGA-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
  "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7996     TCGA-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
  "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
    TCGA-A4-7286     TCGA-A4-7287     TCGA-A4-7288     TCGA-A4-7583 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7585     TCGA-A4-7732     TCGA-A4-7734     TCGA-A4-7915 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-A4-7996     TCGA-AL-3466     TCGA-AL-3467     TCGA-AL-3468 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-AL-3472     TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B3-3925     TCGA-B3-3926     TCGA-B3-4103     TCGA-B3-4104 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4113     TCGA-B9-4114     TCGA-B9-4115     TCGA-B9-4116 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-4117     TCGA-B9-4617     TCGA-B9-5155     TCGA-B9-5156 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-B9-7268     TCGA-BQ-5875     TCGA-BQ-5876     TCGA-BQ-5877 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880     TCGA-BQ-5881 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5883     TCGA-BQ-5884     TCGA-BQ-5885 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5886     TCGA-BQ-5887     TCGA-BQ-5888     TCGA-BQ-5889 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892     TCGA-BQ-5893 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5894     TCGA-BQ-7044     TCGA-BQ-7045     TCGA-BQ-7046 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7048     TCGA-BQ-7049     TCGA-BQ-7050     TCGA-BQ-7051 
  "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7053     TCGA-BQ-7055     TCGA-BQ-7056     TCGA-BQ-7058 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7059     TCGA-BQ-7060     TCGA-BQ-7061     TCGA-BQ-7062 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-5560     TCGA-DW-5561     TCGA-DW-7834     TCGA-DW-7837 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7838     TCGA-DW-7839     TCGA-DW-7840     TCGA-DW-7841 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7842     TCGA-DZ-6131     TCGA-DZ-6132     TCGA-DZ-6133 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
    TCGA-DZ-6134     TCGA-DZ-6135     TCGA-EV-5901     TCGA-EV-5902 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-EV-5903     TCGA-G7-6789     TCGA-G7-6790     TCGA-G7-6792 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-6793     TCGA-G7-6795     TCGA-G7-6796     TCGA-G7-6797 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-7502     TCGA-GL-6846     TCGA-GL-7966 
"LGI4 WILD-TYPE"   "LGI4 MUTATED" "LGI4 WILD-TYPE" 
[1] "hr="     "8.2e+07"
D7V2, continuous
D7V3, binary
                cls
clus              0  1
  LGI4 MUTATED    0  4
  LGI4 WILD-TYPE 31 63
[1] "tbl2"
                cls
clus             [,1] [,2]
  LGI4 MUTATED      0    4
  LGI4 WILD-TYPE   31   63
        clus
vv       LGI4 MUTATED LGI4 WILD-TYPE
  FEMALE            0             31
  MALE              4             63
D7V4, continuous
[1] "Remove cluster labels:" "LGI4 MUTATED"          
clus
  LGI4 MUTATED LGI4 WILD-TYPE 
             1             19 
    TCGA-A4-7286     TCGA-A4-7828     TCGA-AL-3466     TCGA-DW-5560 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7834     TCGA-DW-7837     TCGA-DW-7838     TCGA-DW-7839 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-DW-7840     TCGA-DW-7841     TCGA-DW-7842     TCGA-EV-5901 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-EV-5902     TCGA-EV-5903     TCGA-G7-6790     TCGA-G7-6793 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-6796     TCGA-G7-6797     TCGA-G7-7502 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
                vv
clus             T1 T2 T3+T4
  LGI4 MUTATED    2  0     2
  LGI4 WILD-TYPE 52 12    30
D7V5, multiclass
       clus
vv      LGI4 MUTATED LGI4 WILD-TYPE
  T1               2             52
  T2               0             12
  T3+T4            2             30
                vv
clus             N0 N1 N2
  LGI4 MUTATED    1  1  0
  LGI4 WILD-TYPE 19 10  4
D7V6, multiclass
[1] "Remove cluster labels:" "LGI4 MUTATED"          
clus
  LGI4 MUTATED LGI4 WILD-TYPE 
             2             33 
    TCGA-A4-7583     TCGA-A4-7585     TCGA-A4-7915     TCGA-AL-3466 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-AL-3473     TCGA-AL-7173     TCGA-B1-5398     TCGA-B9-7268 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5877     TCGA-BQ-5878     TCGA-BQ-5879     TCGA-BQ-5880 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5882     TCGA-BQ-5885     TCGA-BQ-5887     TCGA-BQ-5888 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5889     TCGA-BQ-5890     TCGA-BQ-5891     TCGA-BQ-5892 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-5893     TCGA-BQ-5894     TCGA-BQ-7045     TCGA-BQ-7050 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-BQ-7051     TCGA-BQ-7056     TCGA-BQ-7058     TCGA-DZ-6131 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-G7-6789     TCGA-G7-6793     TCGA-G7-6795     TCGA-GL-7966 
"LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" "LGI4 WILD-TYPE" 
    TCGA-J7-6720 
"LGI4 WILD-TYPE" 
                vv
clus             M0 M1 MX
  LGI4 MUTATED    2  0  2
  LGI4 WILD-TYPE 51  5 29
D7V7, multiclass
    clus
vv   LGI4 MUTATED LGI4 WILD-TYPE
  M0            2             51
  M1            0              5
  MX            2             29
                vv
clus              I II III IV
  LGI4 MUTATED    2  0   1  1
  LGI4 WILD-TYPE 47  6  22  8
D7V8, multiclass
     clus
vv    LGI4 MUTATED LGI4 WILD-TYPE
  I              2             47
  II             0              6
  III            1             22
  IV             1              8
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
                "PATHOLOGY.T"                 "PATHOLOGY.N" 
                           V7                            V8 
        "PATHOLOGICSPREAD(M)"                 "TUMOR.STAGE" 
> q(save="no")
