
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_Cnvsarms_onlysig.11.3769/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/146079/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP/1552281/1.GDAC_clinicalDataPicker.Finished/KIRP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP", "-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=KIRP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=95, in cluster file=75, common to both=75
[1] "Reduce the number of clustering variables from 78 to 48."
[1] 48 75
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                69 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                69 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                65 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                65 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11                64 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11                64 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20                55 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               20                55 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                53 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               22                53 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                71 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                71 
[1] "4q gain mutation analysis"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                72 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                72 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                67 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                67 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                66 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                9                66 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                71 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                71 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                72 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                72 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38                37 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               38                37 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               38                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               38                37 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                71 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                71 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                68 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                68 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 72 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 72 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 53 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                22                 53 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                 53 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                22                 53 
[1] "13q gain mutation analysis"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 65 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                10                 65 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                34                 41 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                34                 41 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                 45 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                30                 45 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                34                 41 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                34                 41 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                45                 30 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                45                 30 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 69 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 69 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 71 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 71 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                20                 55 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                20                 55 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                22                 53 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                22                 53 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                68 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                68 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                70 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                70 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                70 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                70 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                70 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                70 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                71 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                4                71 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                72 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                72 
[1] "6p loss mutation analysis"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                68 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                7                68 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                9                66 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                9                66 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                65 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               10                65 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                64 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                64 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                 71 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 4                 71 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 69 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                 69 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 68 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 68 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 70 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 70 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 62 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                13                 62 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 69 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 69 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 72 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 3                 72 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 66 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 66 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 65 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                10                 65 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 65 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 65 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 60 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 60 
[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] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NEOADJUVANTTHERAPY"                    
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 75 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
         293         1778         1636          412          922          763 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 
         336          109          125          179          135         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
          21          329           92           14           33           19 
TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
         196         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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
         353          414         2428         2459         1556         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
        1669          471          178          160          208          977 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
        1257           NA          928         1059          387         5558 
TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 
          NA           NA           NA 
Variable 1:'AGE':	nDistinctValues=34,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=65,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 10:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=3,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=9,	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:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 75 columns, 1 survival variables, and 6 non-survival variables.
AGE, nv=34, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
38  9 27  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   38     9    28 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
38  9 27  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   38     9    28 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
15 10  3 
[1] "table(vv)"
vv
   N0 N1+N2 
   15    13 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 
15 10  3 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 15

$Class1_nSamples
[1] 13

$Class0_label
[1] "N0"

$Class1_label
[1] "N1+N2"


   N0 N1+N2 
   15    13 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED    4  2
  1Q GAIN WILD-TYPE 55 11
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                66 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                11 
$`1Q GAIN MUTATED`
TCGA-AL-3466 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-G7-6789 
        9.63        25.35         7.63         0.95         7.89         6.84 

$`1Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25        10.82        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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.78        11.61        13.61        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 
       61.02        54.87        15.48         5.85         5.26        32.12 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       41.33        11.05        30.51        34.82        12.72       182.73 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.95              0.46 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            25.35            182.73 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            7.760            22.275 
[1] "0.9 - 25.4 (7.8)"   "0.5 - 182.7 (22.3)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
[1] "hr=" "10" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    4
  1Q GAIN WILD-TYPE   20   49
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               2                20
  MALE                 4                49
D1V4, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                1                 9 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5902 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6797 
"1Q GAIN WILD-TYPE" 
D1V5, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1                  0                38
  T2                  0                 9
  T3+T4               6                22
D1V6, multiclass
       clus
vv      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0                  3                12
  N1+N2               3                10
D1V7, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               3                45
  M1               2                 3
  MX               1                13

Clustering(2) Variable = 2p gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    7  3
  2P GAIN WILD-TYPE 52 10
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               10                62 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                3                10 
$`2P GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-4117 TCGA-BQ-5893 TCGA-BQ-7046 TCGA-DW-5561 
        9.63        13.55         0.46         7.89        96.92        13.61 
TCGA-DZ-6133 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
       51.16         6.84        32.12        30.51 

$`2P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
       58.45        53.79        30.31        25.08        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        3.02         1.08         0.62         6.44        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-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.63         0.95        11.97         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       48.26        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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
        3.78        11.61        79.82        80.84        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       15.48         5.85         5.26        41.33        11.05        34.82 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.62 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            96.92            182.73 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           13.580            20.875 
[1] "0.5 - 96.9 (13.6)"  "0.6 - 182.7 (20.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2P GAIN MUTATED"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      3    7
  2P GAIN WILD-TYPE   19   46
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               3                19
  MALE                 7                46
D2V4, continuous
D2V5, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1                  6                32
  T2                  1                 8
  T3+T4               3                25
D2V6, multiclass
       clus
vv      2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0                  1                14
  N1+N2               3                10
D2V7, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               3                45
  M1               2                 3
  MX               4                10

Clustering(3) Variable = 2q gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    8  3
  2Q GAIN WILD-TYPE 51 10
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               11                61 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                10 
$`2Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-4117 TCGA-BQ-5885 TCGA-BQ-5893 TCGA-BQ-7046 
        9.63        13.55         0.46        30.28         7.89        96.92 
TCGA-DW-5561 TCGA-DZ-6133 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
       13.61        51.16         6.84        32.12        30.51 

$`2Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
       58.45        53.79        30.31        25.08        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        3.02         1.08         0.62         6.44        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        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-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       11.61        79.82        80.84        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        5.85         5.26        41.33        11.05        34.82        12.72 
TCGA-GL-6846 
      182.73 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.62 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            96.92            182.73 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            13.61             20.12 
[1] "0.5 - 96.9 (13.6)"  "0.6 - 182.7 (20.1)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "2Q GAIN MUTATED"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3    8
  2Q GAIN WILD-TYPE   19   45
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               3                19
  MALE                 8                45
D3V4, continuous
D3V5, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1                  6                32
  T2                  1                 8
  T3+T4               4                24
D3V6, multiclass
       clus
vv      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0                  2                13
  N1+N2               3                10
D3V7, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               4                44
  M1               2                 3
  MX               4                10

Clustering(4) Variable = 3p gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   16  2
  3P GAIN WILD-TYPE 43 11
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               18                54 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                11 
$`3P GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       53.79        13.55         5.88         0.69         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7045 TCGA-BQ-7046 
        0.62         6.44        47.80        26.04        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DZ-6133 TCGA-G7-6790 TCGA-GL-6846 
        7.00         3.78        11.61        51.16        32.12       182.73 

$`3P GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
        9.63        58.45        30.31        25.08        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5875 
        4.11         4.44        50.50        10.82         3.02        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.23         8.84        63.72        22.92        43.17        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        25.35        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
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-7061 TCGA-DW-5561 TCGA-DZ-6131 
       20.12        11.28         7.63         7.13        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.84        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        6.84        41.33        11.05        30.51        34.82        12.72 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.46              0.95 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           182.73            123.58 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           12.580            20.875 
[1] "0.5 - 182.7 (12.6)" "0.9 - 123.6 (20.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3P GAIN MUTATED"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
[1] "hr=" "1.7"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      3   17
  3P GAIN WILD-TYPE   19   36
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               3                19
  MALE                17                36
D4V4, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                 8 
       TCGA-AL-3466        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5902 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D4V5, multiclass
       clus
vv      3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1                 13                25
  T2                  4                 5
  T3+T4               3                25
D4V6, multiclass
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                26 
       TCGA-AL-3466        TCGA-AL-3473        TCGA-B1-5398        TCGA-BQ-5877 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131        TCGA-G7-6789 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D4V7, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0              11                37
  M1               0                 5
  MX               4                10

Clustering(5) Variable = 3q gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   18  2
  3Q GAIN WILD-TYPE 41 11
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               20                52 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                11 
$`3Q GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       53.79        13.55         5.88         0.69         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7045 
        0.62         6.44        47.80        26.04         7.63        48.26 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       96.92         7.00         3.78        51.16        54.87        15.48 
TCGA-G7-6790 TCGA-GL-6846 
       32.12       182.73 

$`3Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
        9.63        58.45        30.31        25.08        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5875 
        4.11         4.44        50.50        10.82         3.02        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.23         8.84        63.72        22.92        43.17        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        25.35        13.25        10.82 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
        0.95        11.97         7.89         2.76       123.58        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 
       11.28         7.63         7.13        11.61        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 
       80.84        61.02         5.85         5.26         6.84        41.33 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       11.05        30.51        34.82        12.72 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.46              0.95 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           182.73            123.58 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           14.515            20.875 
[1] "0.5 - 182.7 (14.5)" "0.9 - 123.6 (20.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
[1] "hr=" "2.1"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   19
  3Q GAIN WILD-TYPE   19   34
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               3                19
  MALE                19                34
D5V4, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 8 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5902 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D5V5, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1                 14                24
  T2                  4                 5
  T3+T4               4                24
D5V6, multiclass
       clus
vv      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0                  2                13
  N1+N2               1                12
D5V7, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0              12                36
  M1               0                 5
  MX               5                 9

Clustering(6) Variable = 4p gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    3  1
  4P GAIN WILD-TYPE 56 12
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                68 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                12 
$`4P GAIN MUTATED`
TCGA-AL-3466 TCGA-B9-4114 TCGA-G7-6789 TCGA-G7-6795 
        9.63         0.69         6.84        30.51 

$`4P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 
        3.58         4.11         5.88         4.44        50.50        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 
        3.02         0.46         1.08         0.62         6.44        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-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        5.85         5.26        32.12        41.33        11.05        34.82 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.69              0.46 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            30.51            182.73 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            8.235            20.875 
[1] "0.7 - 30.5 (8.2)"   "0.5 - 182.7 (20.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "4.7"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      1    3
  4P GAIN WILD-TYPE   21   50
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               1                21
  MALE                 3                50
D6V4, continuous
[1] "Remove cluster labels:" "4P GAIN MUTATED"       
clus
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                 9 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5902 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6797 
"4P GAIN WILD-TYPE" 
D6V5, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1                  1                37
  T2                  1                 8
  T3+T4               2                26
D6V6, multiclass
       clus
vv      4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0                  1                14
  N1+N2               2                11
D6V7, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               0                48
  M1               1                 4
  MX               2                12

Clustering(7) Variable = 4q gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED    3  0
  4Q GAIN WILD-TYPE 56 13
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                3                69 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                0                13 
$`4Q GAIN MUTATED`
TCGA-B9-4114 TCGA-G7-6789 TCGA-G7-6795 
        0.69         6.84        30.51 

$`4Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.89         2.76       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       13.61        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       15.48         5.85         5.26        32.12        41.33        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.69              0.46 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            30.51            182.73 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             6.84             20.12 
[1] "0.7 - 30.5 (6.8)"   "0.5 - 182.7 (20.1)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "4Q GAIN MUTATED" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
[1] "hr="     "9200000"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      1    2
  4Q GAIN WILD-TYPE   21   51
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               1                21
  MALE                 2                51
D7V4, continuous
D7V5, multiclass
       clus
vv      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1                  1                37
  T2                  1                 8
  T3+T4               1                27
D7V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                26 
       TCGA-AL-3466        TCGA-AL-3473        TCGA-B1-5398        TCGA-BQ-5877 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-GL-6846 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
D7V7, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                65 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-BQ-5875 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-GL-6846        TCGA-HE-7128        TCGA-HE-7129 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HE-7130 
"4Q GAIN WILD-TYPE" 

Clustering(8) Variable = 5p gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    6  1
  5P GAIN WILD-TYPE 53 12
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                7                65 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                12 
$`5P GAIN MUTATED`
TCGA-AL-3466 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5891 TCGA-DZ-6131 TCGA-EV-5902 
        9.63        11.05         0.46         0.95        79.82         5.85 
TCGA-G7-6789 
        6.84 

$`5P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B3-3925 
       58.45        53.79        13.55        30.31        25.08         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        3.02         1.08         0.62         6.44        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-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.63        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 
        7.13         3.78        11.61        13.61        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       61.02        54.87        15.48         5.26        32.12        41.33 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       11.05        30.51        34.82        12.72       182.73 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.46              0.62 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            79.82            182.73 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             6.84             22.92 
[1] "0.5 - 79.8 (6.8)"   "0.6 - 182.7 (22.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      4    4
  5P GAIN WILD-TYPE   18   49
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               4                18
  MALE                 4                49
D8V4, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 8 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5903 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D8V5, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1                  1                37
  T2                  1                 8
  T3+T4               6                22
D8V6, multiclass
       clus
vv      5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0                  3                12
  N1+N2               2                11
D8V7, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               4                44
  M1               1                 4
  MX               2                12

Clustering(9) Variable = 5q gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    7  1
  5Q GAIN WILD-TYPE 52 12
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                64 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                1                12 
$`5Q GAIN MUTATED`
TCGA-AL-3466 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
        9.63        11.05         0.46         7.63         0.95        11.97 
TCGA-EV-5902 TCGA-G7-6789 
        5.85         6.84 

$`5Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B3-3925 
       58.45        53.79        13.55        30.31        25.08         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        3.02         1.08         0.62         6.44        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-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       10.82         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-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       11.61        13.61        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       54.87        15.48         5.26        32.12        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       30.51        34.82        12.72       182.73 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.46              0.62 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            11.97            182.73 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            7.235            25.215 
[1] "0.5 - 12.0 (7.2)"   "0.6 - 182.7 (25.2)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr=" "4.1"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      4    5
  5Q GAIN WILD-TYPE   18   48
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               4                18
  MALE                 5                48
D9V4, continuous
[1] "Remove cluster labels:" "5Q GAIN MUTATED"       
clus
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                 8 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5903 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
D9V5, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1                  2                36
  T2                  1                 8
  T3+T4               6                22
D9V6, multiclass
       clus
vv      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0                  4                11
  N1+N2               2                11
D9V7, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               6                42
  M1               1                 4
  MX               1                13

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    2  2
  6P GAIN WILD-TYPE 57 11
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                4                68 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                11 
$`6P GAIN MUTATED`
TCGA-AL-3466 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-DW-5561 
        9.63         7.89        93.34        13.61 

$`6P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
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-DZ-6131 TCGA-DZ-6132 
        7.00         7.13         3.78        11.61        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        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-GL-6846 
       12.72       182.73 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             7.89              0.46 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            93.34            182.73 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           11.620            20.875 
[1] "7.9 - 93.3 (11.6)"  "0.5 - 182.7 (20.9)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "3.4"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    4
  6P GAIN WILD-TYPE   22   49
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 4                49
D10V4, continuous
[1] "Remove cluster labels:" "6P GAIN MUTATED"       
clus
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                2                 8 
       TCGA-DW-5560        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
D10V5, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1                  1                37
  T2                  0                 9
  T3+T4               3                25
D10V6, multiclass
       clus
vv      6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0                  1                14
  N1+N2               2                11
D10V7, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               2                46
  M1               2                 3
  MX               0                14

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    1  2
  6Q GAIN WILD-TYPE 58 11
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                69 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                11 
$`6Q GAIN MUTATED`
TCGA-AL-3466 TCGA-BQ-5893 TCGA-DW-5561 
        9.63         7.89        13.61 

$`6Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DZ-6131 
        7.63         7.00         7.13         3.78        11.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.26         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             7.89              0.46 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            13.61            182.73 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             9.63             21.63 
[1] "7.9 - 13.6 (9.6)"   "0.5 - 182.7 (21.6)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "15" 
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0    3
  6Q GAIN WILD-TYPE   22   50
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               0                22
  MALE                 3                50
D11V4, continuous
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                 8 
       TCGA-DW-5560        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V5, multiclass
       clus
vv      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1                  1                37
  T2                  0                 9
  T3+T4               2                26
D11V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN MUTATED"       
clus
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                2                26 
       TCGA-AL-3473        TCGA-B1-5398        TCGA-BQ-5877        TCGA-BQ-5878 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882        TCGA-BQ-5885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5894        TCGA-BQ-7045 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
D11V7, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               1                47
  M1               2                 3
  MX               0                14

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   31  5
  7P GAIN WILD-TYPE 28  8
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               36                36 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                5                 8 
$`7P GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4103 
        9.63        53.79        13.55        30.31         3.58         5.88 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50         0.69        10.82         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
        6.44        47.80        26.04        25.35        10.82         0.95 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.58        48.26        96.92        50.37         7.63         7.00 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        7.13        11.61        13.61        80.84        51.16        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-GL-6846 
       15.48         5.26         6.84        32.12        30.51       182.73 

$`7P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
       58.45        25.08        11.05         4.11         4.44         3.02 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       21.63        40.83        30.28        26.04        13.25         7.63 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       11.97         7.89         2.76        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7062 TCGA-DZ-6131 
       49.84        26.27        20.12        11.28         3.78        79.82 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       54.87         5.85        41.33        11.05        34.82        12.72 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.46              2.76 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           182.73             93.34 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           13.580            22.275 
[1] "0.5 - 182.7 (13.6)" "2.8 - 93.3 (22.3)" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
[1] "hr=" "1.5"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8   30
  7P GAIN WILD-TYPE   14   23
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               8                14
  MALE                30                23
D12V4, continuous
D12V5, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1                 23                15
  T2                  6                 3
  T3+T4               9                19
D12V6, multiclass
       clus
vv      7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0                  5                10
  N1+N2               4                 9
D12V7, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              21                27
  M1               2                 3
  MX               8                 6

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   31  4
  7Q GAIN WILD-TYPE 28  9
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               35                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                4                 9 
$`7Q GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4103 TCGA-B9-4113 
       53.79        13.55        30.31         3.58         5.88        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
        0.69        10.82         0.46         1.08         0.62         6.44 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-7044 
       47.80        26.04        25.35        10.82         0.95       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       48.26        96.92        50.37         7.63         7.00         7.13 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
       11.61        13.61        80.84        51.16        61.02        15.48 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-GL-6846 
        5.26         6.84        32.12        30.51       182.73 

$`7Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 
        9.63        58.45        25.08        11.05         4.11         4.44 
TCGA-B9-4116 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        3.02        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       43.17        21.63        40.83        30.28        26.04        13.25 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 
        7.63        11.97         7.89         2.76        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7062 
       61.28        49.84        26.27        20.12        11.28         3.78 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       79.82        54.87         5.85        41.33        11.05        34.82 
TCGA-G7-6797 
       12.72 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.46              2.76 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           182.73             93.34 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            13.61             21.63 
[1] "0.5 - 182.7 (13.6)" "2.8 - 93.3 (21.6)" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
[1] "hr=" "2.1"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9   29
  7Q GAIN WILD-TYPE   13   24
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               9                13
  MALE                29                24
D13V4, continuous
D13V5, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1                 23                15
  T2                  6                 3
  T3+T4               9                19
D13V6, multiclass
       clus
vv      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0                  5                10
  N1+N2               3                10
D13V7, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              22                26
  M1               1                 4
  MX               8                 6

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    3  1
  8P GAIN WILD-TYPE 56 12
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4                68 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                12 
$`8P GAIN MUTATED`
TCGA-AL-3471 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-G7-6789 
       13.55        43.17        25.35         6.84 

$`8P GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
        9.63        58.45        53.79        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 
       86.73        19.23         8.84        63.72        22.92        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        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-5561 TCGA-DZ-6131 
        7.00         7.13         3.78        11.61        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        5.26        32.12        41.33        11.05        30.51        34.82 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             6.84              0.46 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            43.17            182.73 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           19.450            19.675 
[1] "6.8 - 43.2 (19.5)"  "0.5 - 182.7 (19.7)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    3
  8P GAIN WILD-TYPE   21   50
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               1                21
  MALE                 3                50
D14V4, continuous
D14V5, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1                  1                37
  T2                  0                 9
  T3+T4               3                25
D14V6, multiclass
       clus
vv      8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0                  1                14
  N1+N2               2                11
D14V7, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               3                45
  M1               0                 5
  MX               1                13

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    4  3
  8Q GAIN WILD-TYPE 55 10
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                7                65 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                3                10 
$`8Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3471 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-G7-6789 
        9.63        13.55        43.17        25.35        20.12         6.84 
TCGA-G7-6793 
       11.05 

$`8Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 
       58.45        53.79        30.31        25.08        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 
        3.02         0.46         1.08         0.62         6.44        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       19.23         8.84        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.78        11.61        13.61        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 
       61.02        54.87        15.48         5.85         5.26        32.12 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       41.33        30.51        34.82        12.72       182.73 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.84              0.46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            43.17            182.73 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            13.55             21.63 
[1] "6.8 - 43.2 (13.6)"  "0.5 - 182.7 (21.6)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "5.2"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      3    4
  8Q GAIN WILD-TYPE   19   49
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               3                19
  MALE                 4                49
D15V4, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                2                 8 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901        TCGA-EV-5902 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6796        TCGA-G7-6797 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D15V5, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1                  1                37
  T2                  0                 9
  T3+T4               6                22
D15V6, multiclass
       clus
vv      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0                  2                13
  N1+N2               4                 9
D15V7, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               4                44
  M1               1                 4
  MX               2                12

Clustering(16) Variable = 10p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    2  0
  10P GAIN WILD-TYPE 57 13
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 70 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 0                 13 
$`10P GAIN MUTATED`
TCGA-AL-3468 TCGA-B9-4617 
       53.79         1.08 

$`10P GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
        9.63        58.45        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 
       10.82         3.02         0.46         0.62         6.44        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-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        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-GL-6846 
       30.51        34.82        12.72       182.73 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.08               0.46 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             53.79             182.73 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            27.435             19.675 
[1] "1.1 - 53.8 (27.4)"  "0.5 - 182.7 (19.7)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 70 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-BQ-5875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-6846 
"10P GAIN WILD-TYPE" 
D16V2, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 70 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-BQ-5875 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-6846 
"10P GAIN WILD-TYPE" 
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1    2
  10P GAIN WILD-TYPE   21   51
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  2                 51
D16V4, continuous
D16V5, multiclass
       clus
vv      10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                   1                 37
  T2                   1                  8
  T3+T4                1                 27
D16V6, multiclass
D16V7, multiclass
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 65 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3471 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-BQ-5875         TCGA-BQ-5876 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 

Clustering(17) Variable = 12p gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   17  4
  12P GAIN WILD-TYPE 42  9
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                21                 51 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 4                  9 
$`12P GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 
       53.79        13.55         3.58        50.50         0.69         1.08 
TCGA-B9-5156 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7059 
        6.44         8.84        43.17        25.35         0.95         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        7.13         3.78        13.61        80.84        51.16        61.02 
TCGA-G7-6789 TCGA-G7-6795 TCGA-GL-6846 
        6.84        30.51       182.73 

$`12P GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 
        9.63        58.45        30.31        25.08        11.05         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        5.88         4.44        10.82         3.02         0.46         0.62 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       86.73        19.23        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63        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-7060 TCGA-DW-5560 TCGA-DZ-6131 
       26.27        20.12        11.28         7.00        11.61        79.82 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       54.87        15.48         5.85         5.26        32.12        41.33 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       11.05        34.82        12.72 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.69               0.46 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            182.73             123.58 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             13.55              21.63 
[1] "0.7 - 182.7 (13.6)" "0.5 - 123.6 (21.6)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12P GAIN MUTATED"   "12P GAIN MUTATED"   "12P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
[1] "hr=" "1.1"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      4   18
  12P GAIN WILD-TYPE   18   35
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 18                 35
D17V4, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-EV-5901 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D17V5, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                  13                 25
  T2                   2                  7
  T3+T4                7                 21
D17V6, multiclass
       clus
vv      12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0                   3                 12
  N1+N2                4                  9
D17V7, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0               10                 38
  M1                1                  4
  MX                7                  7

Clustering(18) Variable = 12q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   17  4
  12Q GAIN WILD-TYPE 42  9
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                21                 51 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 4                  9 
$`12Q GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 
       53.79        13.55         3.58        50.50         0.69         1.08 
TCGA-B9-5156 TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7059 
        6.44         8.84        43.17        25.35         0.95         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        7.13         3.78        13.61        80.84        51.16        61.02 
TCGA-G7-6789 TCGA-G7-6795 TCGA-GL-6846 
        6.84        30.51       182.73 

$`12Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 
        9.63        58.45        30.31        25.08        11.05         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
        5.88         4.44        10.82         3.02         0.46         0.62 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       86.73        19.23        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.82 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.63        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-7060 TCGA-DW-5560 TCGA-DZ-6131 
       26.27        20.12        11.28         7.00        11.61        79.82 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       54.87        15.48         5.85         5.26        32.12        41.33 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       11.05        34.82        12.72 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.69               0.46 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            182.73             123.58 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             13.55              21.63 
[1] "0.7 - 182.7 (13.6)" "0.5 - 123.6 (21.6)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "12Q GAIN MUTATED"   "12Q GAIN MUTATED"   "12Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      4   18
  12Q GAIN WILD-TYPE   18   35
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                4                 18
  MALE                 18                 35
D18V4, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-EV-5901 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D18V5, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                  13                 25
  T2                   2                  7
  T3+T4                7                 21
D18V6, multiclass
       clus
vv      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                   3                 12
  N1+N2                4                  9
D18V7, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0               10                 38
  M1                1                  4
  MX                7                  7

Clustering(19) Variable = 13q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    8  1
  13Q GAIN WILD-TYPE 51 12
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 9                 63 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 12 
$`13Q GAIN MUTATED`
TCGA-B1-5398 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 
       11.05         0.46         1.08        96.92        13.61        51.16 
TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6796 
        5.26        32.12        34.82 

$`13Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
       10.82         3.02         0.62         6.44        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-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.58        48.26        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
        7.13         3.78        11.61        79.82        80.84        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       54.87        15.48         5.85         6.84        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-6846 
       30.51        12.72       182.73 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.46               0.62 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             96.92             182.73 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             13.61              20.12 
[1] "0.5 - 96.9 (13.6)"  "0.6 - 182.7 (20.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "13Q GAIN MUTATED"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE"   "13Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "13Q GAIN MUTATED" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      3    7
  13Q GAIN WILD-TYPE   19   46
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                3                 19
  MALE                  7                 46
D19V4, continuous
D19V5, multiclass
       clus
vv      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                   7                 31
  T2                   1                  8
  T3+T4                2                 26
D19V6, multiclass
[1] "Remove cluster labels:" "13Q GAIN MUTATED"      
clus
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 27 
        TCGA-AL-3466         TCGA-AL-3473         TCGA-BQ-5877 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DZ-6131         TCGA-G7-6789 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-GL-6846 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
D19V7, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                5                 43
  M1                0                  5
  MX                3                 11

Clustering(20) Variable = 16p gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   27  5
  16P GAIN WILD-TYPE 32  8
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                32                 40 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 5                  8 
$`16P GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B9-4114 
        9.63        53.79        13.55        11.05         5.88         0.69 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5881 
        0.46         1.08         0.62         6.44        86.73        47.80 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 
       26.04        25.35         7.63         0.95         7.89       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 
       48.26        96.92        50.37        11.28         7.00         3.78 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.16        61.02         5.85         5.26         6.84        32.12 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

$`16P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
       58.45        30.31        25.08         3.58         4.11         4.44 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       50.50        10.82         3.02        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.17        21.63        40.83        26.04        30.28 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 
       13.25        10.82        11.97         2.76        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 
       61.28        49.84        26.27        20.12         7.63         7.13 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 
       11.61        13.61        79.82        80.84        54.87        15.48 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
       41.33        11.05        30.51        34.82 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.46               2.76 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            182.73              93.34 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            11.165             24.000 
[1] "0.5 - 182.7 (11.2)" "2.8 - 93.3 (24.0)" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16P GAIN MUTATED"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16P GAIN MUTATED"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED"   "16P GAIN MUTATED" 
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      5   29
  16P GAIN WILD-TYPE   17   24
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                5                 17
  MALE                 29                 24
D20V4, continuous
D20V5, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                  16                 22
  T2                   5                  4
  T3+T4               13                 15
D20V6, multiclass
       clus
vv      16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                   6                  9
  N1+N2                5                  8
D20V7, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0               20                 28
  M1                2                  3
  MX                7                  7

Clustering(21) Variable = 16q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   26  2
  16Q GAIN WILD-TYPE 33 11
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                28                 44 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 11 
$`16Q GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       53.79        13.55        11.05         5.88         0.69         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5886 
        1.08         0.62         6.44        86.73        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
       25.35         0.95       123.58        48.26        96.92        50.37 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 
        7.00         3.78        51.16        61.02         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 TCGA-GL-6846 
        6.84        32.12        12.72       182.73 

$`16Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B3-3925 TCGA-B3-3926 
        9.63        58.45        30.31        25.08         3.58         4.11 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5877 
        4.44        50.50        10.82         3.02        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 
       30.28        13.25        10.82         7.63        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
        2.76        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       20.12        11.28         7.63         7.13        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-G7-6792 TCGA-G7-6793 
       79.82        80.84        54.87        15.48        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6796 
       30.51        34.82 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.46               2.76 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            182.73              93.34 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            13.135             20.875 
[1] "0.5 - 182.7 (13.1)" "2.8 - 93.3 (20.9)" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "16Q GAIN MUTATED"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED"   "16Q GAIN MUTATED" 
[1] "hr=" "3.7"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      5   25
  16Q GAIN WILD-TYPE   17   28
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                5                 17
  MALE                 25                 28
D21V4, continuous
D21V5, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                  16                 22
  T2                   5                  4
  T3+T4                9                 19
D21V6, multiclass
       clus
vv      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0                   5                 10
  N1+N2                2                 11
D21V7, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0               18                 30
  M1                0                  5
  MX                7                  7

Clustering(22) Variable = 17p gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   28  4
  17P GAIN WILD-TYPE 31  9
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                32                 40 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 4                  9 
$`17P GAIN MUTATED`
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       53.79        13.55        30.31         3.58         5.88         4.44 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50         0.69        10.82         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-BQ-5881 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
        6.44        47.80         0.95        11.97         7.89        48.26 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       96.92        50.37         7.00         3.78        11.61        13.61 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6795 
       51.16        61.02        15.48         5.26        32.12        30.51 
TCGA-G7-6796 TCGA-GL-6846 
       34.82       182.73 

$`17P GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4116 
        9.63        58.45        25.08        11.05         4.11         3.02 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
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-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       13.25        10.82         7.63         2.76       123.58        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 
        7.63         7.13        79.82        80.84        54.87         5.85 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6797 
        6.84        41.33        11.05        12.72 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.46               2.76 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            182.73             123.58 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             12.76              24.00 
[1] "0.5 - 182.7 (12.8)" "2.8 - 123.6 (24.0)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17P GAIN MUTATED"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17P GAIN MUTATED"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED"   "17P GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17P GAIN MUTATED" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
[1] "hr=" "1.5"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      5   29
  17P GAIN WILD-TYPE   17   24
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                5                 17
  MALE                 29                 24
D22V4, continuous
D22V5, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                  22                 16
  T2                   7                  2
  T3+T4                5                 23
D22V6, multiclass
       clus
vv      17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                   5                 10
  N1+N2                2                 11
D22V7, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0               19                 29
  M1                1                  4
  MX                7                  7

Clustering(23) Variable = 17q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   35  8
  17Q GAIN WILD-TYPE 24  5
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                43                 29 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                  5 
$`17Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B3-3925 TCGA-B3-4103 
        9.63        53.79        13.55        30.31         3.58         5.88 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
        4.44        50.50         0.69        10.82         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 
        0.62         6.44        86.73        43.17        47.80        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 
       13.25         7.63         0.95        11.97         7.89        48.26 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 
       96.92        50.37        49.84        11.28         7.00         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
       11.61        13.61        79.82        51.16        61.02        15.48 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        5.26         6.84        32.12        11.05        30.51        34.82 
TCGA-GL-6846 
      182.73 

$`17Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5876 
       58.45        25.08        11.05         4.11         3.02        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.84        63.72        22.92        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       30.28        25.35        10.82         2.76       123.58        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 
       44.84        61.28        26.27        20.12         7.63         7.13 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6797 
       80.84        54.87         5.85        41.33        12.72 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.46               2.76 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            182.73             123.58 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             13.25              25.08 
[1] "0.5 - 182.7 (13.2)" "2.8 - 123.6 (25.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED"   "17Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "1.3"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     10   35
  17Q GAIN WILD-TYPE   12   18
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               10                 12
  MALE                 35                 18
D23V4, continuous
[1] "Remove cluster labels:" "17Q GAIN WILD-TYPE"    
clus
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                  2 
      TCGA-AL-3466       TCGA-DW-5560       TCGA-DW-5561       TCGA-EV-5901 
"17Q GAIN MUTATED" "17Q GAIN MUTATED" "17Q GAIN MUTATED" "17Q GAIN MUTATED" 
      TCGA-EV-5903       TCGA-G7-6790       TCGA-G7-6793       TCGA-G7-6796 
"17Q GAIN MUTATED" "17Q GAIN MUTATED" "17Q GAIN MUTATED" "17Q GAIN MUTATED" 
D23V5, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                  23                 15
  T2                   7                  2
  T3+T4               15                 13
D23V6, multiclass
       clus
vv      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                   8                  7
  N1+N2                7                  6
D23V7, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               26                 22
  M1                2                  3
  MX               10                  4

Clustering(24) Variable = 18p gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    5  1
  18P GAIN WILD-TYPE 54 12
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 6                 66 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 12 
$`18P GAIN MUTATED`
TCGA-AL-3466 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
        9.63         5.88         4.44         0.62        11.61        32.12 

$`18P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        3.58         4.11        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.46         1.08         6.44        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-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.13         3.78        13.61        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-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       41.33        11.05        30.51        34.82        12.72       182.73 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.62               0.46 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             32.12             182.73 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             7.755             22.275 
[1] "0.6 - 32.1 (7.8)"   "0.5 - 182.7 (22.3)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18P GAIN MUTATED"   "18P GAIN MUTATED" "18P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18P GAIN MUTATED" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "3"  
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    5
  18P GAIN WILD-TYPE   21   48
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 48
D24V4, continuous
D24V5, multiclass
       clus
vv      18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                   3                 35
  T2                   1                  8
  T3+T4                2                 26
D24V6, multiclass
[1] "Remove cluster labels:" "18P GAIN MUTATED"      
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 1                 27 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-BQ-5877 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DZ-6131         TCGA-G7-6789 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
D24V7, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                3                 45
  M1                1                  4
  MX                1                 13

Clustering(25) Variable = 18q gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    4  0
  18Q GAIN WILD-TYPE 55 13
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 4                 68 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 0                 13 
$`18Q GAIN MUTATED`
TCGA-B3-4103 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 
        5.88         0.62        11.61        32.12 

$`18Q GAIN WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         4.11         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-BQ-5875 
       10.82         3.02         0.46         1.08         6.44        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-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DZ-6131 
        7.63         7.00         7.13         3.78        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        5.26         6.84        41.33        11.05        30.51        34.82 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.62               0.46 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             32.12             182.73 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             8.745             20.875 
[1] "0.6 - 32.1 (8.7)"   "0.5 - 182.7 (20.9)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    3
  18Q GAIN WILD-TYPE   21   50
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 21
  MALE                  3                 50
D25V4, continuous
[1] "Remove cluster labels:" "18Q GAIN MUTATED"      
clus
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                  8 
        TCGA-AL-3466         TCGA-DW-5561         TCGA-EV-5901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6793 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
D25V5, multiclass
       clus
vv      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                   3                 35
  T2                   0                  9
  T3+T4                1                 27
D25V6, multiclass
D25V7, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                2                 46
  M1                0                  5
  MX                1                 13

Clustering(26) Variable = 20p gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   18  2
  20P GAIN WILD-TYPE 41 11
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                20                 52 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                 11 
$`20P GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3925 TCGA-B3-4103 TCGA-B9-4117 
        9.63        53.79        13.55         3.58         5.88         0.46 
TCGA-B9-4617 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 
        1.08        25.35         0.95        96.92        50.37         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6789 
       11.61        13.61        80.84        51.16         5.85         6.84 
TCGA-G7-6795 TCGA-G7-6797 
       30.51        12.72 

$`20P GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 
       58.45        30.31        25.08        11.05         4.11         4.44 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 
       50.50         0.69        10.82         3.02         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.82         7.63        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
      123.58        48.26        93.34        44.84        61.28        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-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 
       79.82        61.02        54.87        15.48         5.26        32.12 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-GL-6846 
       41.33        11.05        34.82       182.73 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.46               0.62 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             96.92             182.73 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            12.165             24.000 
[1] "0.5 - 96.9 (12.2)"  "0.6 - 182.7 (24.0)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20P GAIN MUTATED"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      5   15
  20P GAIN WILD-TYPE   17   38
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                5                 17
  MALE                 15                 38
D26V4, continuous
D26V5, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                  12                 26
  T2                   3                  6
  T3+T4                5                 23
D26V6, multiclass
       clus
vv      20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                   4                 11
  N1+N2                2                 11
D26V7, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0               12                 36
  M1                1                  4
  MX                5                  9

Clustering(27) Variable = 20q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   19  2
  20Q GAIN WILD-TYPE 40 11
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 51 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 2                 11 
$`20Q GAIN MUTATED`
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
        9.63        53.79        13.55         3.58         5.88         4.44 
TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7046 TCGA-BQ-7051 
        0.46         1.08        25.35         0.95        96.92        50.37 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 
        3.78        11.61        13.61        80.84        51.16         5.85 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 
        6.84        30.51        12.72 

$`20Q GAIN WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-4113 
       58.45        30.31        25.08        11.05         4.11        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 
        0.69        10.82         3.02         0.62         6.44        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-5888 
       21.63        40.83        26.04        30.28        26.04        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.63        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
       48.26        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DZ-6131 
       20.12        11.28         7.63         7.00         7.13        79.82 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       61.02        54.87        15.48         5.26        32.12        41.33 
TCGA-G7-6793 TCGA-G7-6796 TCGA-GL-6846 
       11.05        34.82       182.73 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.46               0.62 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             96.92             182.73 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             11.61              25.08 
[1] "0.5 - 96.9 (11.6)"  "0.6 - 182.7 (25.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6   16
  20Q GAIN WILD-TYPE   16   37
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 16
  MALE                 16                 37
D27V4, continuous
D27V5, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                  12                 26
  T2                   4                  5
  T3+T4                6                 22
D27V6, multiclass
       clus
vv      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                   4                 11
  N1+N2                2                 11
D27V7, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               14                 34
  M1                1                  4
  MX                5                  9

Clustering(28) Variable = 1p loss mutation analysis
D28V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    5  2
  1P LOSS WILD-TYPE 54 11
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                7                65 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                11 
$`1P LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-7044 TCGA-BQ-7055 
        4.11        86.73         8.84        21.63       123.58        26.27 
TCGA-G7-6797 
       12.72 

$`1P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.23        63.72        22.92        43.17        47.80        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-5894 TCGA-BQ-7045 
        7.63         0.95        11.97         7.89         2.76        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-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       11.61        13.61        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-GL-6846 
       41.33        11.05        30.51        34.82       182.73 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             4.11              0.46 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           123.58            182.73 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            21.63             19.23 
[1] "4.1 - 123.6 (21.6)" "0.5 - 182.7 (19.2)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      2    5
  1P LOSS WILD-TYPE   20   48
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               2                20
  MALE                 5                48
D28V4, continuous
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                1                 9 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6796 
"1P LOSS WILD-TYPE" 
D28V5, multiclass
       clus
vv      1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1                  3                35
  T2                  0                 9
  T3+T4               4                24
D28V6, multiclass
[1] "Remove cluster labels:" "1P LOSS MUTATED"       
clus
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                2                26 
       TCGA-AL-3466        TCGA-AL-3473        TCGA-B1-5398        TCGA-BQ-5878 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5885        TCGA-BQ-5887 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7058        TCGA-DZ-6131        TCGA-G7-6789        TCGA-G7-6793 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-GL-6846 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
D28V7, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               5                43
  M1               1                 4
  MX               1                13

Clustering(29) Variable = 3p loss mutation analysis
D29V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 56 11
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                67 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                11 
$`3P LOSS MUTATED`
TCGA-AL-3473 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 
       25.08         8.84        21.63        11.97        79.82 

$`3P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-5398 
        9.63        58.45        53.79        13.55        30.31        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.73        19.23        63.72        22.92        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.63         0.95         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 
        7.13         3.78        11.61        13.61        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-GL-6846 
      182.73 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             8.84              0.46 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            79.82            182.73 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            21.63             19.23 
[1] "8.8 - 79.8 (21.6)"  "0.5 - 182.7 (19.2)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      0    5
  3P LOSS WILD-TYPE   22   48
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               0                22
  MALE                 5                48
D29V4, continuous
D29V5, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1                  1                37
  T2                  1                 8
  T3+T4               3                25
D29V6, multiclass
       clus
vv      3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0                  3                12
  N1+N2               2                11
D29V7, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               3                45
  M1               1                 4
  MX               1                13

Clustering(30) Variable = 4p loss mutation analysis
D30V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    2  2
  4P LOSS WILD-TYPE 57 11
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                68 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                11 
$`4P LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-DZ-6131 
        4.11        22.92        21.63        79.82 

$`4P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.73        19.23         8.84        63.72        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        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-5561 TCGA-DZ-6132 
        7.00         7.13         3.78        11.61        13.61        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        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-GL-6846 
       12.72       182.73 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             4.11              0.46 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            79.82            182.73 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           22.275            17.355 
[1] "4.1 - 79.8 (22.3)"  "0.5 - 182.7 (17.4)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    2
  4P LOSS WILD-TYPE   19   51
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                19
  MALE                 2                51
D30V4, continuous
D30V5, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1                  1                37
  T2                  0                 9
  T3+T4               4                24
D30V6, multiclass
       clus
vv      4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0                  2                13
  N1+N2               1                12
D30V7, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               4                44
  M1               0                 5
  MX               1                13

Clustering(31) Variable = 4q loss mutation analysis
D31V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  1
  4Q LOSS WILD-TYPE 56 12
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                4                68 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                12 
$`4Q LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 
        4.11        19.23        21.63        79.82 

$`4Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.73         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        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-5561 TCGA-DZ-6132 
        7.00         7.13         3.78        11.61        13.61        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        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-GL-6846 
       12.72       182.73 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             4.11              0.46 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            79.82            182.73 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            20.43             17.80 
[1] "4.1 - 79.8 (20.4)"  "0.5 - 182.7 (17.8)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      2    3
  4Q LOSS WILD-TYPE   20   50
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               2                20
  MALE                 3                50
D31V4, continuous
D31V5, multiclass
       clus
vv      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1                  2                36
  T2                  0                 9
  T3+T4               3                25
D31V6, multiclass
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                2                26 
       TCGA-AL-3466        TCGA-AL-3473        TCGA-B1-5398        TCGA-BQ-5877 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5885 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-G7-6789        TCGA-G7-6793 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-GL-6846 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
D31V7, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               4                44
  M1               0                 5
  MX               1                13

Clustering(32) Variable = 5p loss mutation analysis
D32V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    1  2
  5P LOSS WILD-TYPE 58 11
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                69 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                11 
$`5P LOSS MUTATED`
TCGA-BQ-5879 TCGA-BQ-5894 TCGA-G7-6793 
       22.92         2.76        11.05 

$`5P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
        6.44        86.73        19.23         8.84        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.89       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        5.85         5.26         6.84        32.12        41.33        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.76              0.46 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.92            182.73 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            11.05             20.12 
[1] "2.8 - 22.9 (11.1)"  "0.5 - 182.7 (20.1)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr=" "9.2"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2    2
  5P LOSS WILD-TYPE   20   51
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               2                20
  MALE                 2                51
D32V4, continuous
[1] "Remove cluster labels:" "5P LOSS MUTATED"       
clus
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 9 
       TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561        TCGA-EV-5901 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6796 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6797 
"5P LOSS WILD-TYPE" 
D32V5, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1                  0                38
  T2                  1                 8
  T3+T4               3                25
D32V6, multiclass
       clus
vv      5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0                  0                15
  N1+N2               3                10
D32V7, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               2                46
  M1               1                 4
  MX               1                13

Clustering(33) Variable = 5q loss mutation analysis
D33V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    2  1
  5Q LOSS WILD-TYPE 57 12
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                69 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                12 
$`5Q LOSS MUTATED`
TCGA-BQ-5879 TCGA-BQ-5894 TCGA-DZ-6131 
       22.92         2.76        79.82 

$`5Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
        6.44        86.73        19.23         8.84        63.72        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.89       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.26         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.76              0.46 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            79.82            182.73 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            22.92             19.23 
[1] "2.8 - 79.8 (22.9)"  "0.5 - 182.7 (19.2)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    2
  5Q LOSS WILD-TYPE   21   51
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               1                21
  MALE                 2                51
D33V4, continuous
D33V5, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1                  0                38
  T2                  0                 9
  T3+T4               3                25
D33V6, multiclass
       clus
vv      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0                  1                14
  N1+N2               2                11
D33V7, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               1                47
  M1               1                 4
  MX               1                13

Clustering(34) Variable = 6p loss mutation analysis
D34V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED    4  2
  6P LOSS WILD-TYPE 55 11
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                6                66 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                2                11 
$`6P LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5882 TCGA-BQ-7056 TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-6797 
        4.11        21.63        20.12         5.85        11.05        12.72 

$`6P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        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-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.37        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 
        7.00         7.13         3.78        11.61        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       80.84        51.16        61.02        54.87        15.48         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
        6.84        32.12        41.33        30.51        34.82       182.73 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             4.11              0.46 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            21.63            182.73 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           11.885            24.000 
[1] "4.1 - 21.6 (11.9)"  "0.5 - 182.7 (24.0)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6P LOSS MUTATED" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"   "6P LOSS MUTATED" "6P LOSS WILD-TYPE" 
[1] "hr=" "5.3"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      4    3
  6P LOSS WILD-TYPE   18   50
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               4                18
  MALE                 3                50
D34V4, continuous
D34V5, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1                  3                35
  T2                  0                 9
  T3+T4               4                24
D34V6, multiclass
       clus
vv      6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0                  2                13
  N1+N2               1                12
D34V7, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               5                43
  M1               0                 5
  MX               2                12

Clustering(35) Variable = 6q loss mutation analysis
D35V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    6  2
  6Q LOSS WILD-TYPE 53 11
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                64 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                11 
$`6Q LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-7056 TCGA-EV-5902 
        4.11        86.73        21.63        13.25        20.12         5.85 
TCGA-G7-6793 TCGA-G7-6797 
       11.05        12.72 

$`6Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
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-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.78        11.61        13.61        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       61.02        54.87        15.48         5.26         6.84        32.12 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
       41.33        30.51        34.82       182.73 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             4.11              0.46 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            86.73            182.73 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           12.985            24.000 
[1] "4.1 - 86.7 (13.0)"  "0.5 - 182.7 (24.0)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      6    3
  6Q LOSS WILD-TYPE   16   50
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               6                16
  MALE                 3                50
D35V4, continuous
D35V5, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1                  4                34
  T2                  0                 9
  T3+T4               5                23
D35V6, multiclass
       clus
vv      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0                  3                12
  N1+N2               1                12
D35V7, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               7                41
  M1               0                 5
  MX               2                12

Clustering(36) Variable = 9p loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    6  3
  9P LOSS WILD-TYPE 53 10
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                9                63 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                3                10 
$`9P LOSS MUTATED`
TCGA-AL-3466 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-7056 
        9.63         4.11         3.02        22.92        13.25        20.12 
TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-6796 
       79.82        11.05        34.82 

$`9P LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        3.58         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        0.46         1.08         0.62         6.44        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        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-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       26.27        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       11.61        13.61        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       15.48         5.85         5.26         6.84        32.12        41.33 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-6846 
       30.51        12.72       182.73 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             3.02              0.46 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            79.82            182.73 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            13.25             21.63 
[1] "3.0 - 79.8 (13.2)"  "0.5 - 182.7 (21.6)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "2.9"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7    3
  9P LOSS WILD-TYPE   15   50
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               7                15
  MALE                 3                50
D36V4, continuous
D36V5, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1                  3                35
  T2                  1                 8
  T3+T4               6                22
D36V6, multiclass
       clus
vv      9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0                  3                12
  N1+N2               3                10
D36V7, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               5                43
  M1               1                 4
  MX               3                11

Clustering(37) Variable = 9q loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    7  3
  9Q LOSS WILD-TYPE 52 10
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               10                62 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                3                10 
$`9Q LOSS MUTATED`
TCGA-AL-3466 TCGA-B3-3926 TCGA-B3-4104 TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-7055 
        9.63         4.11         4.44        22.92        13.25        26.27 
TCGA-BQ-7056 TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-6796 
       20.12        79.82        11.05        34.82 

$`9Q LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        3.58         5.88        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 
        0.46         1.08         0.62         6.44        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        43.17        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        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-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       13.61        80.84        51.16        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        5.85         5.26         6.84        32.12        41.33        30.51 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             4.11              0.46 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            79.82            182.73 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           16.685            20.430 
[1] "4.1 - 79.8 (16.7)"  "0.5 - 182.7 (20.4)"
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-3473        TCGA-B1-5398        TCGA-B3-3925 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B9-4113 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116        TCGA-B9-4117 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156        TCGA-BQ-5875 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "2.5"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      6    5
  9Q LOSS WILD-TYPE   16   48
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               6                16
  MALE                 5                48
D37V4, continuous
D37V5, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1                  4                34
  T2                  1                 8
  T3+T4               6                22
D37V6, multiclass
       clus
vv      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0                  3                12
  N1+N2               3                10
D37V7, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               7                41
  M1               1                 4
  MX               3                11

Clustering(38) Variable = 10q loss mutation analysis
D38V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    1  2
  10Q LOSS WILD-TYPE 58 11
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 69 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 11 
$`10Q LOSS MUTATED`
TCGA-AL-3466 TCGA-BQ-5876 TCGA-BQ-5882 
        9.63        19.23        21.63 

$`10Q LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.73         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.82         7.63         0.95        11.97         7.89         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.58        48.26        96.92        93.34        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-5561 TCGA-DZ-6131 
        7.00         7.13         3.78        11.61        13.61        79.82 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.84        51.16        61.02        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.26         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              9.63               0.46 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             21.63             182.73 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             19.23              20.12 
[1] "9.6 - 21.6 (19.2)"  "0.5 - 182.7 (20.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "8.1"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      1    3
  10Q LOSS WILD-TYPE   21   50
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  3                 50
D38V4, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-EV-5901 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D38V5, multiclass
       clus
vv      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                   1                 37
  T2                   0                  9
  T3+T4                3                 25
D38V6, multiclass
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                 26 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-BQ-5877 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-GL-6846 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
D38V7, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                3                 45
  M1                1                  4
  MX                0                 14

Clustering(39) Variable = 11p loss mutation analysis
D39V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    3  2
  11P LOSS WILD-TYPE 56 11
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 67 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 11 
$`11P LOSS MUTATED`
TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-7044 
        4.44        19.23         8.84        21.63       123.58 

$`11P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         4.11         5.88        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.73        63.72        22.92        43.17        47.80        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-5894 TCGA-BQ-7045 
        7.63         0.95        11.97         7.89         2.76        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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.78        11.61        13.61        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-GL-6846 
      182.73 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              4.44               0.46 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            123.58             182.73 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             19.23              20.12 
[1] "4.4 - 123.6 (19.2)" "0.5 - 182.7 (20.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      1    5
  11P LOSS WILD-TYPE   21   48
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                1                 21
  MALE                  5                 48
D39V4, continuous
D39V5, multiclass
       clus
vv      11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                   1                 37
  T2                   1                  8
  T3+T4                4                 24
D39V6, multiclass
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 2                 26 
        TCGA-AL-3466         TCGA-AL-3473         TCGA-B1-5398 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-GL-6846 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D39V7, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                5                 43
  M1                1                  4
  MX                0                 14

Clustering(40) Variable = 11q loss mutation analysis
D40V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    3  3
  11Q LOSS WILD-TYPE 56 10
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 6                 66 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 10 
$`11Q LOSS MUTATED`
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-G7-6793 
       19.23         8.84        21.63         7.63       123.58        11.05 

$`11Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
        6.44        86.73        63.72        22.92        43.17        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       10.82         0.95        11.97         7.89         2.76        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-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.78        11.61        13.61        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-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       32.12        41.33        30.51        34.82        12.72       182.73 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              7.63               0.46 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.58             182.73 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             15.14              21.52 
[1] "7.6 - 123.6 (15.1)" "0.5 - 182.7 (21.5)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "4.2"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    5
  11Q LOSS WILD-TYPE   20   48
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                2                 20
  MALE                  5                 48
D40V4, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D40V5, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                   1                 37
  T2                   0                  9
  T3+T4                6                 22
D40V6, multiclass
       clus
vv      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                   2                 13
  N1+N2                2                 11
D40V7, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                5                 43
  M1                1                  4
  MX                1                 13

Clustering(41) Variable = 13q loss mutation analysis
D41V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    2  3
  13Q LOSS WILD-TYPE 57 10
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 5                 67 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 3                 10 
$`13Q LOSS MUTATED`
TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-G7-6793 
        4.11        86.73        22.92        21.63        11.05 

$`13Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       11.05         3.58         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.23         8.84        63.72        43.17        47.80        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-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 
        7.13         3.78        11.61        13.61        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        6.84        32.12        41.33        30.51        34.82        12.72 
TCGA-GL-6846 
      182.73 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              4.11               0.46 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             86.73             182.73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             21.63              19.23 
[1] "4.1 - 86.7 (21.6)"  "0.5 - 182.7 (19.2)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "4"  
D41V2, continuous
D41V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    1
  13Q LOSS WILD-TYPE   18   52
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 18
  MALE                  1                 52
D41V4, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D41V5, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                   1                 37
  T2                   0                  9
  T3+T4                4                 24
D41V6, multiclass
       clus
vv      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                   1                 14
  N1+N2                2                 11
D41V7, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                4                 44
  M1                0                  5
  MX                1                 13

Clustering(42) Variable = 14q loss mutation analysis
D42V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED    9  3
  14Q LOSS WILD-TYPE 50 10
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                12                 60 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 3                 10 
$`14Q LOSS MUTATED`
TCGA-AL-3466 TCGA-AL-3473 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5880 
        9.63        25.08         4.11         3.02        19.23        43.17 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-G7-6793 TCGA-G7-6796 
       30.28        13.25        79.82        80.84        11.05        34.82 

$`14Q LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-5398 TCGA-B3-3925 
       58.45        53.79        13.55        30.31        11.05         3.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
        5.88         4.44        50.50         0.69        10.82         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
        1.08         0.62         6.44        86.73         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       22.92        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        10.82         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.58        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.37        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.00         7.13         3.78        11.61        13.61 
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-G7-6795 TCGA-G7-6797 TCGA-GL-6846 
        6.84        32.12        41.33        30.51        12.72       182.73 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              3.02               0.46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             80.84             182.73 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            22.155             17.800 
[1] "3.0 - 80.8 (22.2)"  "0.5 - 182.7 (17.8)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      5    8
  14Q LOSS WILD-TYPE   17   45
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                5                 17
  MALE                  8                 45
D42V4, continuous
D42V5, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                   5                 33
  T2                   2                  7
  T3+T4                6                 22
D42V6, multiclass
       clus
vv      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0                   3                 12
  N1+N2                4                  9
D42V7, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                7                 41
  M1                1                  4
  MX                4                 10

Clustering(43) Variable = 15q loss mutation analysis
D43V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    3  2
  15Q LOSS WILD-TYPE 56 11
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 5                 67 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 11 
$`15Q LOSS MUTATED`
TCGA-B1-5398 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-G7-6796 
       11.05         4.11        22.92        21.63        34.82 

$`15Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        25.08 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        3.58         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5875 
        3.02         0.46         1.08         0.62         6.44        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.23         8.84        63.72        43.17        47.80        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-5894 TCGA-BQ-7044 
        7.63         0.95        11.97         7.89         2.76       123.58 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.37 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 
        7.13         3.78        11.61        13.61        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 
        6.84        32.12        41.33        11.05        30.51        12.72 
TCGA-GL-6846 
      182.73 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              4.11               0.46 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             34.82             182.73 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             21.63              19.23 
[1] "4.1 - 34.8 (21.6)"  "0.5 - 182.7 (19.2)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "4"  
D43V2, continuous
D43V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      3    3
  15Q LOSS WILD-TYPE   19   50
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  3                 50
D43V4, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6797 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
D43V5, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                   2                 36
  T2                   0                  9
  T3+T4                4                 24
D43V6, multiclass
       clus
vv      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                   2                 13
  N1+N2                1                 12
D43V7, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                5                 43
  M1                0                  5
  MX                1                 13

Clustering(44) Variable = 17p loss mutation analysis
D44V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    0  2
  17P LOSS WILD-TYPE 59 11
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 70 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 11 
$`17P LOSS MUTATED`
TCGA-AL-3466 TCGA-G7-6793 
        9.63        11.05 

$`17P LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
        3.58         4.11         5.88         4.44        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.82         3.02         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.73        19.23         8.84        63.72        22.92        43.17 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.82         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.89         2.76       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.00         7.13         3.78        11.61 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       13.61        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       15.48         5.85         5.26         6.84        32.12        41.33 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       30.51        34.82        12.72       182.73 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              9.63               0.46 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             11.05             182.73 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            10.340             20.875 
[1] "9.6 - 11.1 (10.3)"  "0.5 - 182.7 (20.9)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 70 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B1-5398 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-6846 
"17P LOSS WILD-TYPE" 
D44V2, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 70 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-B1-5398 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B9-4113         TCGA-B9-4114 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DZ-6131         TCGA-DZ-6132 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-6846 
"17P LOSS WILD-TYPE" 
D44V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    1
  17P LOSS WILD-TYPE   20   52
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                2                 20
  MALE                  1                 52
D44V4, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                  8 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-EV-5901 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6790 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D44V5, multiclass
       clus
vv      17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                   0                 38
  T2                   0                  9
  T3+T4                3                 25
D44V6, multiclass
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 2                 26 
        TCGA-AL-3473         TCGA-B1-5398         TCGA-BQ-5877 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DZ-6131         TCGA-G7-6789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D44V7, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                1                 47
  M1                1                  4
  MX                1                 13

Clustering(45) Variable = 18p loss mutation analysis
D45V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    5  4
  18P LOSS WILD-TYPE 54  9
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 9                 63 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                  9 
$`18P LOSS MUTATED`
TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-7044 
        3.02         8.84        22.92        21.63        25.35       123.58 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-EV-5903 
       11.28         7.63         5.26 

$`18P LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
        0.69        10.82         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.73        19.23        63.72        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89         2.76        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-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       20.12         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.85         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              3.02               0.46 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.58             182.73 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             11.28              20.12 
[1] "3.0 - 123.6 (11.3)" "0.5 - 182.7 (20.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "4.7"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      2    7
  18P LOSS WILD-TYPE   20   46
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                2                 20
  MALE                  7                 46
D45V4, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-G7-6790 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D45V5, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                   2                 36
  T2                   1                  8
  T3+T4                6                 22
D45V6, multiclass
       clus
vv      18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                   2                 13
  N1+N2                3                 10
D45V7, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                7                 41
  M1                1                  4
  MX                0                 14

Clustering(46) Variable = 18q loss mutation analysis
D46V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  4
  18Q LOSS WILD-TYPE 54  9
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 63 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                  9 
$`18Q LOSS MUTATED`
TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-7044 
        3.02         8.84        22.92        21.63        25.35       123.58 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-EV-5903 
       11.28         7.63         5.26 

$`18Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        53.79        13.55        30.31        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-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
        0.69        10.82         0.46         1.08         0.62         6.44 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.73        19.23        63.72        43.17        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.89         2.76        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-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       20.12         7.00         7.13         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.82        80.84        51.16        61.02        54.87        15.48 
TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.85         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-6846 
       34.82        12.72       182.73 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              3.02               0.46 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.58             182.73 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             11.28              20.12 
[1] "3.0 - 123.6 (11.3)" "0.5 - 182.7 (20.1)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "4.7"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3    7
  18Q LOSS WILD-TYPE   19   46
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  7                 46
D46V4, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-G7-6790 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D46V5, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                   2                 36
  T2                   1                  8
  T3+T4                7                 21
D46V6, multiclass
       clus
vv      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                   2                 13
  N1+N2                3                 10
D46V7, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                8                 40
  M1                1                  4
  MX                0                 14

Clustering(47) Variable = 21q loss mutation analysis
D47V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   10  0
  21Q LOSS WILD-TYPE 49 13
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 62 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                 13 
$`21Q LOSS MUTATED`
TCGA-AL-3468 TCGA-B3-3925 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5885 TCGA-BQ-5890 
       53.79         3.58         4.11        86.73        30.28         7.63 
TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-G7-6796 
        2.76         7.13        61.02        34.82 

$`21Q LOSS WILD-TYPE`
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
        9.63        58.45        13.55        30.31        25.08        11.05 
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-BQ-5876 TCGA-BQ-5877 
        0.46         1.08         0.62         6.44        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-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 
       26.04        26.04        25.35        13.25        10.82         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.89       123.58        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.37        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.00         3.78        11.61        13.61 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.82        80.84        51.16        54.87        15.48         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        5.26         6.84        32.12        41.33        11.05        30.51 
TCGA-G7-6797 TCGA-GL-6846 
       12.72       182.73 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              2.76               0.46 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             86.73             182.73 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            18.955             19.675 
[1] "2.8 - 86.7 (19.0)"  "0.5 - 182.7 (19.7)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr="     "8.5e+07"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3    7
  21Q LOSS WILD-TYPE   19   46
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                3                 19
  MALE                  7                 46
D47V4, continuous
[1] "Remove cluster labels:" "21Q LOSS MUTATED"      
clus
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 1                  9 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6797 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
D47V5, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                   4                 34
  T2                   1                  8
  T3+T4                5                 23
D47V6, multiclass
       clus
vv      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                   2                 13
  N1+N2                1                 12
D47V7, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                7                 41
  M1                1                  4
  MX                2                 12

Clustering(48) Variable = 22q loss mutation analysis
D48V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   12  3
  22Q LOSS WILD-TYPE 47 10
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 57 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 3                 10 
$`22Q LOSS MUTATED`
TCGA-AL-3466 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5890 
        9.63         4.11        86.73         8.84        26.04         7.63 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 
        2.76       123.58        61.28        20.12         7.13        79.82 
TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-6797 
        5.85        11.05        12.72 

$`22Q LOSS WILD-TYPE`
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
       58.45        53.79        13.55        30.31        25.08        11.05 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        3.58         5.88         4.44        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-BQ-5876 
        3.02         0.46         1.08         0.62         6.44        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-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 
       30.28        26.04        25.35        13.25        10.82         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
       11.97         7.89        48.26        96.92        93.34        44.84 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.37        49.84        26.27        11.28         7.63         7.00 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.78        11.61        13.61        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       54.87        15.48         5.26         6.84        32.12        41.33 
TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
       30.51        34.82       182.73 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              2.76               0.46 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            123.58             182.73 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             11.05              22.92 
[1] "2.8 - 123.6 (11.1)" "0.5 - 182.7 (22.9)"
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B9-4113 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-BQ-5875         TCGA-BQ-5876 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DZ-6131 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-GL-6846 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      7    8
  22Q LOSS WILD-TYPE   15   45
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                7                 15
  MALE                  8                 45
D48V4, continuous
D48V5, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                   6                 32
  T2                   0                  9
  T3+T4                9                 19
D48V6, multiclass
       clus
vv      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                   4                 11
  N1+N2                4                  9
D48V7, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                9                 39
  M1                3                  2
  MX                3                 11
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
                "PATHOLOGY.T"                 "PATHOLOGY.N" 
                           V7 
        "PATHOLOGICSPREAD(M)" 
> q(save="no")
