
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/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/KIRP-TP/3142216/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/KIRP-TP/3132656/1.GDAC_clinicalDataPicker.Finished/KIRP-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=KIRP-TP", "-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-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=104, in cluster file=127, common to both=104
[1] "Reduce the number of clustering variables from 80 to 58."
[1]  58 104
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                8                96 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                8                96 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
               11                93 
      2P GAIN CNV 2P GAIN WILD-TYPE 
               11                93 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               13                91 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               13                91 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
               24                80 
      3P GAIN CNV 3P GAIN WILD-TYPE 
               24                80 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               26                78 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               26                78 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               100 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4               100 
[1] "4q gain"
[1] 3
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               101 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3               101 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               10                94 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               10                94 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               10                94 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               10                94 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               100 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4               100 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3               101 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3               101 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               55                49 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               55                49 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               56                48 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               56                48 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                5                99 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                5                99 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                97 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                97 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 4                100 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 4                100 
[1] "10q gain"
[1] 3
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                101 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                101 
[1] "12p gain"
[1] 3
      12P GAIN CNV 12P GAIN WILD-TYPE 
                31                 73 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                31                 73 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                31                 73 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                31                 73 
[1] "13q gain"
[1] 3
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                11                 93 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                11                 93 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                44                 60 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                44                 60 
[1] "16q gain"
[1] 3
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                41                 63 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                41                 63 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                52                 52 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                52                 52 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                62                 42 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                62                 42 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 6                 98 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 6                 98 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                100 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                100 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                31                 73 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                31                 73 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                32                 72 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                32                 72 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4               100 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4               100 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               11                93 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               11                93 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                6                98 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                6                98 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                6                98 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                6                98 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3               101 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3               101 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
                8                96 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                8                96 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                9                95 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                9                95 
[1] "5p loss"
[1] 3
      5P LOSS CNV 5P LOSS WILD-TYPE 
                4               100 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                4               100 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4               100 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4               100 
[1] "6p loss"
[1] 3
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9                95 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                9                95 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               10                94 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               10                94 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               101 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3               101 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               13                91 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               13                91 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               13                91 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               13                91 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 98 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 98 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 6                 98 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 6                 98 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 8                 96 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 8                 96 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 9                 95 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 9                 95 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 95 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 95 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                19                 85 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                19                 85 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                10                 94 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                10                 94 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 3                101 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 3                101 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 5                 99 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 5                 99 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                15                 89 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                15                 89 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                16                 88 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                16                 88 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                100 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                100 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                101 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                101 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                11                 93 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                11                 93 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                20                 84 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                20                 84 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               101 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3               101 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "KARNOFSKYPERFORMANCESCORE"             
[11] "HISTOLOGICALTYPE"                      
[12] "PATHOLOGICSPREAD(PT)"                  
[13] "PATHOLOGICSPREAD(PN)"                  
[14] "PATHOLOGICSPREAD(M)"                   
[15] "TUMORSTAGE"                            
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "NUMBERPACKYEARSSMOKED"                 
[18] "TOBACCOSMOKINGHISTORYINDICATOR"        
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 104 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
           1           21          485            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 
           1           27           NA            7           49          140 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
         293         1778         1636          412          922          763 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
        1357          336          223          109          125          179 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         135          147         1536           21          329           92 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
          14           33           19          196           36         2638 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         585          269         1938          697         1313         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
         658         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403          329          232           29          364          240 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3759           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1532         1516          799          612           NA 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          213          217          115          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          418          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
         445           92         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-G7-7501 
        1257           NA          928         1059          387          445 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-7128 TCGA-HE-7129 
         428         5558           NA          112           NA           NA 
TCGA-HE-7130 TCGA-J7-6720 
          NA           NA 
Variable 1:'AGE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=86,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=3,	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=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 11:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'PATHOLOGY.T':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'PATHOLOGY.N':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'PATHOLOGICSPREAD(M)':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'NUMBERPACKYEARSSMOKED':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                         "GENDER"                     
[3] "KARNOFSKY.PERFORMANCE.SCORE" "PATHOLOGY.T"                
[5] "PATHOLOGY.N"                 "PATHOLOGICSPREAD(M)"        
[7] "TUMOR.STAGE"                
[1] "TUMOR.?STAGE" "7"           
[1] "stage2"
vv
 1  2  3  4 
53  7 24  9 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 104 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=39, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=4, binary=FALSE, numeric=TRUE
PATHOLOGY.T, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
58 13 32  1 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
   58    13    33 
$ClinVariableName
[1] "PATHOLOGY.T"

$Table
vv
T1 T2 T3 T4 
58 13 32  1 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
   58    13    33 
PATHOLOGY.N, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
20 12  4 
[1] "table(vv)"
vv
N0 N1 N2 
20 12  4 
$ClinVariableName
[1] "PATHOLOGY.N"

$Table
vv
N0 N1 N2 
20 12  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
20 12  4 
PATHOLOGICSPREAD(M), nv=3, binary=FALSE, numeric=FALSE
TUMOR.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('TUMOR.?STAGE$',vnm)"
vv
  I  II III  IV 
 53   7  24   9 
[1] "table(vv)"
vv
  I  II III  IV 
 53   7  24   9 
$ClinVariableName
[1] "TUMOR.STAGE"

$Table
vv
  I  II III  IV 
 53   7  24   9 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


  I  II III  IV 
 53   7  24   9 

Clustering(1) Variable = 1q gain
D1V1, survival
                   sevent
clus2                0  1
  1Q GAIN CNV        5  2
  1Q GAIN WILD-TYPE 78 12
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                7                90 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                2                12 
$`1Q GAIN CNV`
TCGA-A4-7287 TCGA-AL-3466 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
        0.69         9.63        25.35         7.63         0.95         7.89 
TCGA-G7-6789 
        6.84 

$`1Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.23         1.61         4.60        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        13.25        10.82        11.97         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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-G7-6795 
        5.85         5.26        32.12        41.33        11.05        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       34.82        12.72        14.63        14.07       182.73         3.68 

      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             0.69              0.03 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
            25.35            182.73 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             7.63             14.63 
[1] "0.7 - 25.4 (7.6)"   "0.0 - 182.7 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"1Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"1Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"1Q GAIN WILD-TYPE" 
[1] "hr=" "13" 
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV          4    4
  1Q GAIN WILD-TYPE   30   66
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  FEMALE           4                30
  MALE             4                66
D1V4, continuous
[1] "Remove cluster labels:" "1Q GAIN CNV"           
clus
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G7-7502 
"1Q GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  1Q GAIN CNV        1  0     7
  1Q GAIN WILD-TYPE 57 13    26
D1V5, multiclass
       clus
vv      1Q GAIN CNV 1Q GAIN WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           7                26
                   vv
clus                N0 N1 N2
  1Q GAIN CNV        3  2  1
  1Q GAIN WILD-TYPE 17 10  3
D1V6, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  N0           3                17
  N1           2                10
  N2           1                 3
                   vv
clus                M0 M1 MX
  1Q GAIN CNV        4  2  2
  1Q GAIN WILD-TYPE 50  3 34
D1V7, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  M0           4                50
  M1           2                 3
  MX           2                34
                   vv
clus                 I II III IV
  1Q GAIN CNV        1  0   4  3
  1Q GAIN WILD-TYPE 52  7  20  6
D1V8, multiclass
     clus
vv    1Q GAIN CNV 1Q GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           4                20
  IV            3                 6

Clustering(2) Variable = 2p gain
D2V1, survival
                   sevent
clus2                0  1
  2P GAIN CNV        8  3
  2P GAIN WILD-TYPE 75 11
      2P GAIN CNV 2P GAIN WILD-TYPE 
               11                86 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                3                11 
$`2P GAIN CNV`
TCGA-AL-3466 TCGA-AL-3471 TCGA-B1-7332 TCGA-B9-4117 TCGA-BQ-5893 TCGA-BQ-7046 
        9.63        13.55         7.33         0.46         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 

$`2P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        3.02         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
       13.25        10.82         7.63         0.95        11.97         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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.13         3.78        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       24.46        13.74         3.75        14.63         3.02        79.82 
TCGA-DZ-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-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       41.33        11.05        34.82        12.72        14.63        14.07 
TCGA-GL-6846 TCGA-GL-7966 
      182.73         3.68 

      2P GAIN CNV 2P GAIN WILD-TYPE 
             0.46              0.03 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            96.92            182.73 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            13.55             14.35 
[1] "0.5 - 96.9 (13.6)"  "0.0 - 182.7 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          4    7
  2P GAIN WILD-TYPE   30   63
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  FEMALE           4                30
  MALE             7                63
D2V4, continuous
                   vv
clus                T1 T2 T3+T4
  2P GAIN CNV        6  2     3
  2P GAIN WILD-TYPE 52 11    30
D2V5, multiclass
       clus
vv      2P GAIN CNV 2P GAIN WILD-TYPE
  T1              6                52
  T2              2                11
  T3+T4           3                30
                   vv
clus                N0 N1 N2
  2P GAIN CNV        1  2  1
  2P GAIN WILD-TYPE 19 10  3
D2V6, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  N0           1                19
  N1           2                10
  N2           1                 3
                   vv
clus                M0 M1 MX
  2P GAIN CNV        3  2  5
  2P GAIN WILD-TYPE 51  3 31
D2V7, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  M0           3                51
  M1           2                 3
  MX           5                31
                   vv
clus                 I II III IV
  2P GAIN CNV        6  1   0  3
  2P GAIN WILD-TYPE 47  6  24  6
D2V8, multiclass
     clus
vv    2P GAIN CNV 2P GAIN WILD-TYPE
  I             6                47
  II            1                 6
  III           0                24
  IV            3                 6

Clustering(3) Variable = 2q gain
D3V1, survival
                   sevent
clus2                0  1
  2Q GAIN CNV       10  3
  2Q GAIN WILD-TYPE 73 11
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
               13                84 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                3                11 
$`2Q GAIN CNV`
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-7332 TCGA-B9-4117 TCGA-BQ-5893 
        9.63        13.55        44.61         7.33         0.46         7.89 
TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
       96.92        13.61        51.16         6.84        32.12        30.51 
TCGA-G7-7502 
       14.07 

$`2Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       30.31        25.08        11.05         3.58         4.11         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        4.44         4.83        50.50         0.69        10.82         3.02 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
        1.08         0.62         6.44         1.18        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.84        63.72        22.92        43.17        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
        3.78        11.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6792 
       61.02        54.87        15.48         5.85         5.26        41.33 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       11.05        34.82        12.72        14.63       182.73         3.68 

      2Q GAIN CNV 2Q GAIN WILD-TYPE 
             0.46              0.03 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
            96.92            182.73 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
           13.610            14.185 
[1] "0.5 - 96.9 (13.6)"  "0.0 - 182.7 (14.2)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"2Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          5    8
  2Q GAIN WILD-TYPE   29   62
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  FEMALE           5                29
  MALE             8                62
D3V4, continuous
                   vv
clus                T1 T2 T3+T4
  2Q GAIN CNV        7  2     4
  2Q GAIN WILD-TYPE 51 11    29
D3V5, multiclass
       clus
vv      2Q GAIN CNV 2Q GAIN WILD-TYPE
  T1              7                51
  T2              2                11
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  2Q GAIN CNV        1  2  2
  2Q GAIN WILD-TYPE 19 10  2
D3V6, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  N0           1                19
  N1           2                10
  N2           2                 2
                   vv
clus                M0 M1 MX
  2Q GAIN CNV        4  2  6
  2Q GAIN WILD-TYPE 50  3 30
D3V7, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  M0           4                50
  M1           2                 3
  MX           6                30
                   vv
clus                 I II III IV
  2Q GAIN CNV        7  1   0  4
  2Q GAIN WILD-TYPE 46  6  24  5
D3V8, multiclass
     clus
vv    2Q GAIN CNV 2Q GAIN WILD-TYPE
  I             7                46
  II            1                 6
  III           0                24
  IV            4                 5

Clustering(4) Variable = 3p gain
D4V1, survival
                   sevent
clus2                0  1
  3P GAIN CNV       20  2
  3P GAIN WILD-TYPE 63 12
      3P GAIN CNV 3P GAIN WILD-TYPE 
               22                75 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                2                12 
$`3P GAIN CNV`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       53.79        13.55         7.33         5.88         0.69         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-5886 
        1.08         0.62         6.44         1.18        47.80        26.04 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 
       48.26        96.92         7.00         3.78        11.61        35.93 
TCGA-DW-7838 TCGA-DZ-6133 TCGA-G7-6790 TCGA-GL-6846 
       24.46        51.16        32.12       182.73 

$`3P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5875 
        4.44         4.83        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-DW-7834 
       20.12        11.28         7.63         7.13        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       37.55        13.74         3.75        14.63         3.02        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 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       14.63        14.07         3.68 

      3P GAIN CNV 3P GAIN WILD-TYPE 
             0.46              0.03 
      3P GAIN CNV 3P GAIN WILD-TYPE 
           182.73            129.86 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            12.58             14.07 
[1] "0.5 - 182.7 (12.6)" "0.0 - 129.9 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3P GAIN CNV" "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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-GL-7966 
"3P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3P GAIN CNV" "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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-GL-7966 
"3P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3P GAIN CNV"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3P GAIN CNV" "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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV"       "3P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" 
       TCGA-GL-7966 
"3P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          4   20
  3P GAIN WILD-TYPE   30   50
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  FEMALE           4                30
  MALE            20                50
D4V4, continuous
                   vv
clus                T1 T2 T3+T4
  3P GAIN CNV       15  6     3
  3P GAIN WILD-TYPE 43  7    30
D4V5, multiclass
       clus
vv      3P GAIN CNV 3P GAIN WILD-TYPE
  T1             15                43
  T2              6                 7
  T3+T4           3                30
                   vv
clus                N0 N1 N2
  3P GAIN CNV        2  1  0
  3P GAIN WILD-TYPE 18 11  4
D4V6, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  N0           2                18
  N1           1                11
  N2           0                 4
                   vv
clus                M0 M1 MX
  3P GAIN CNV       12  0  7
  3P GAIN WILD-TYPE 42  5 29
D4V7, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  M0          12                42
  M1           0                 5
  MX           7                29
                   vv
clus                 I II III IV
  3P GAIN CNV       14  2   2  1
  3P GAIN WILD-TYPE 39  5  22  8
D4V8, multiclass
     clus
vv    3P GAIN CNV 3P GAIN WILD-TYPE
  I            14                39
  II            2                 5
  III           2                22
  IV            1                 8

Clustering(5) Variable = 3q gain
D5V1, survival
                   sevent
clus2                0  1
  3Q GAIN CNV       22  2
  3Q GAIN WILD-TYPE 61 12
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
               24                73 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                2                12 
$`3Q GAIN CNV`
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4117 
       53.79        13.55         7.33         5.88         0.69         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-5886 
        1.08         0.62         6.44         1.18        47.80        26.04 
TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 
        7.63        48.26        96.92         7.00         3.78        35.93 
TCGA-DW-7838 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-G7-6790 TCGA-GL-6846 
       24.46        51.16        54.87        15.48        32.12       182.73 

$`3Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5875 
        4.44         4.83        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-DW-7834 
       11.28         7.63         7.13        11.61        13.61       129.86 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       37.55        13.74         3.75        14.63         3.02        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 TCGA-G7-7501 TCGA-G7-7502 
       11.05        30.51        34.82        12.72        14.63        14.07 
TCGA-GL-7966 
        3.68 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
             0.46              0.03 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
           182.73            129.86 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
           14.515            13.740 
[1] "0.5 - 182.7 (14.5)" "0.0 - 129.9 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-GL-7966 
"3Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-GL-7966 
"3Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "3Q GAIN CNV"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV"       "3Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" 
       TCGA-GL-7966 
"3Q GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          4   22
  3Q GAIN WILD-TYPE   30   48
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  FEMALE           4                30
  MALE            22                48
D5V4, continuous
                   vv
clus                T1 T2 T3+T4
  3Q GAIN CNV       16  6     4
  3Q GAIN WILD-TYPE 42  7    29
D5V5, multiclass
       clus
vv      3Q GAIN CNV 3Q GAIN WILD-TYPE
  T1             16                42
  T2              6                 7
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  3Q GAIN CNV        3  1  0
  3Q GAIN WILD-TYPE 17 11  4
D5V6, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  N0           3                17
  N1           1                11
  N2           0                 4
                   vv
clus                M0 M1 MX
  3Q GAIN CNV       13  0  8
  3Q GAIN WILD-TYPE 41  5 28
D5V7, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  M0          13                41
  M1           0                 5
  MX           8                28
                   vv
clus                 I II III IV
  3Q GAIN CNV       15  2   3  1
  3Q GAIN WILD-TYPE 38  5  21  8
D5V8, multiclass
     clus
vv    3Q GAIN CNV 3Q GAIN WILD-TYPE
  I            15                38
  II            2                 5
  III           3                21
  IV            1                 8

Clustering(6) Variable = 4p gain
D6V1, survival
                   sevent
clus2                0  1
  4P GAIN CNV        3  1
  4P GAIN WILD-TYPE 80 13
      4P GAIN CNV 4P GAIN WILD-TYPE 
                4                93 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                13 
$`4P GAIN CNV`
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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       32.12        41.33        11.05        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             0.69              0.03 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            30.51            182.73 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            8.235            14.070 
[1] "0.7 - 30.5 (8.2)"   "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4P GAIN WILD-TYPE" 
[1] "hr=" "5.7"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          1    3
  4P GAIN WILD-TYPE   33   67
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           1                33
  MALE             3                67
D6V4, continuous
[1] "Remove cluster labels:" "4P GAIN CNV"           
clus
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G7-7502 
"4P GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  4P GAIN CNV        1  1     2
  4P GAIN WILD-TYPE 57 12    31
D6V5, multiclass
       clus
vv      4P GAIN CNV 4P GAIN WILD-TYPE
  T1              1                57
  T2              1                12
  T3+T4           2                31
                   vv
clus                N0 N1 N2
  4P GAIN CNV        1  1  1
  4P GAIN WILD-TYPE 19 11  3
D6V6, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  N0           1                19
  N1           1                11
  N2           1                 3
                   vv
clus                M0 M1 MX
  4P GAIN CNV        0  1  2
  4P GAIN WILD-TYPE 54  4 34
D6V7, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  M0           0                54
  M1           1                 4
  MX           2                34
                   vv
clus                 I II III IV
  4P GAIN CNV        1  0   0  2
  4P GAIN WILD-TYPE 52  7  24  7
D6V8, multiclass
     clus
vv    4P GAIN CNV 4P GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           0                24
  IV            2                 7

Clustering(7) Variable = 4q gain
D7V1, survival
                   sevent
clus2                0  1
  4Q GAIN CNV        3  0
  4Q GAIN WILD-TYPE 80 14
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                3                94 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                0                14 
$`4Q GAIN CNV`
TCGA-B9-4114 TCGA-G7-6789 TCGA-G7-6795 
        0.69         6.84        30.51 

$`4Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33         3.58         4.11         5.88         4.44         4.83 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       50.50        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       24.46        13.74         3.75        14.63         3.02        79.82 
TCGA-DZ-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-G7-6796 TCGA-G7-6797 
        5.26        32.12        41.33        11.05        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      4Q GAIN CNV 4Q GAIN WILD-TYPE 
             0.69              0.03 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
            30.51            182.73 
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
            6.840            13.905 
[1] "0.7 - 30.5 (6.8)"   "0.0 - 182.7 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        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-5881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        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-5881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        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-5881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        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-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE"       "4Q GAIN CNV" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"4Q GAIN WILD-TYPE" 
[1] "hr="     "9200000"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN CNV          1    2
  4Q GAIN WILD-TYPE   33   68
        clus
vv       4Q GAIN CNV 4Q GAIN WILD-TYPE
  FEMALE           1                33
  MALE             2                68
D7V4, continuous
                   vv
clus                T1 T2 T3+T4
  4Q GAIN CNV        1  1     1
  4Q GAIN WILD-TYPE 57 12    32
D7V5, multiclass
       clus
vv      4Q GAIN CNV 4Q GAIN WILD-TYPE
  T1              1                57
  T2              1                12
  T3+T4           1                32
                   vv
clus                N0 N1 N2
  4Q GAIN CNV        1  0  1
  4Q GAIN WILD-TYPE 19 12  3
D7V6, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2                34 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3466 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6131        TCGA-G7-6793        TCGA-G7-7501        TCGA-GL-6846 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-J7-6720 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
                   vv
clus                M0 M1 MX
  4Q GAIN CNV        0  0  2
  4Q GAIN WILD-TYPE 54  5 34
D7V7, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2                93 
       TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583        TCGA-A4-7584 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7828 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B3-8121        TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5881        TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5893        TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7046        TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7058        TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7062        TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6132        TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-J7-6720 
"4Q GAIN WILD-TYPE" 
                   vv
clus                 I II III IV
  4Q GAIN CNV        1  0   0  1
  4Q GAIN WILD-TYPE 52  7  24  8
D7V8, multiclass
[1] "Remove cluster labels:" "4Q GAIN CNV"           
clus
      4Q GAIN CNV 4Q GAIN WILD-TYPE 
                2                91 
       TCGA-A4-7287        TCGA-A4-7583        TCGA-A4-7584        TCGA-A4-7585 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-7734        TCGA-A4-7828        TCGA-A4-7915        TCGA-A4-7996 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3471        TCGA-AL-3473 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4115        TCGA-B9-5155        TCGA-B9-7268 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877        TCGA-BQ-5878 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881        TCGA-BQ-5882 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885        TCGA-BQ-5886 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046        TCGA-BQ-7048 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051        TCGA-BQ-7053 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-BQ-7059 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062        TCGA-DW-5560 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6792        TCGA-G7-6793 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7773        TCGA-GL-7966        TCGA-HE-7128 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-HE-7129        TCGA-HE-7130        TCGA-J7-6720 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(8) Variable = 5p gain
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN CNV        8  1
  5P GAIN WILD-TYPE 75 13
      5P GAIN CNV 5P GAIN WILD-TYPE 
                9                88 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                1                13 
$`5P GAIN CNV`
TCGA-A4-8098 TCGA-AL-3466 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5891 TCGA-DW-7838 
        4.60         9.63        11.05         0.46         0.95        24.46 
TCGA-DZ-6131 TCGA-EV-5902 TCGA-G7-6789 
       79.82         5.85         6.84 

$`5P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.89         0.23         1.61        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61         7.33         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        3.02         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-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-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-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        13.74         3.75        14.63         3.02 
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-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             0.46              0.03 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            79.82            182.73 
      5P GAIN CNV 5P GAIN WILD-TYPE 
             6.84             14.63 
[1] "0.5 - 79.8 (6.8)"   "0.0 - 182.7 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          4    6
  5P GAIN WILD-TYPE   30   64
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  FEMALE           4                30
  MALE             6                64
D8V4, continuous
                   vv
clus                T1 T2 T3+T4
  5P GAIN CNV        3  1     6
  5P GAIN WILD-TYPE 55 12    27
D8V5, multiclass
       clus
vv      5P GAIN CNV 5P GAIN WILD-TYPE
  T1              3                55
  T2              1                12
  T3+T4           6                27
                   vv
clus                N0 N1 N2
  5P GAIN CNV        3  1  1
  5P GAIN WILD-TYPE 17 11  3
D8V6, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  N0           3                17
  N1           1                11
  N2           1                 3
                   vv
clus                M0 M1 MX
  5P GAIN CNV        4  1  4
  5P GAIN WILD-TYPE 50  4 32
D8V7, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  M0           4                50
  M1           1                 4
  MX           4                32
                   vv
clus                 I II III IV
  5P GAIN CNV        3  0   4  2
  5P GAIN WILD-TYPE 50  7  20  7
D8V8, multiclass
     clus
vv    5P GAIN CNV 5P GAIN WILD-TYPE
  I             3                50
  II            0                 7
  III           4                20
  IV            2                 7

Clustering(9) Variable = 5q gain
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN CNV        8  1
  5Q GAIN WILD-TYPE 75 13
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                9                88 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                1                13 
$`5Q GAIN CNV`
TCGA-A4-8098 TCGA-AL-3466 TCGA-B1-5398 TCGA-B9-4117 TCGA-BQ-5891 TCGA-BQ-5892 
        4.60         9.63        11.05         0.46         0.95        11.97 
TCGA-DW-7838 TCGA-EV-5902 TCGA-G7-6789 
       24.46         5.85         6.84 

$`5Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        0.89         0.23         1.61        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61         7.33         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        3.02         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       13.25        10.82         7.63         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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       37.55        13.74         3.75        14.63         3.02        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-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             0.46              0.03 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            24.46            182.73 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            6.840            15.055 
[1] "0.5 - 24.5 (6.8)"   "0.0 - 182.7 (15.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"5Q GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          4    6
  5Q GAIN WILD-TYPE   30   64
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  FEMALE           4                30
  MALE             6                64
D9V4, continuous
                   vv
clus                T1 T2 T3+T4
  5Q GAIN CNV        4  1     5
  5Q GAIN WILD-TYPE 54 12    28
D9V5, multiclass
       clus
vv      5Q GAIN CNV 5Q GAIN WILD-TYPE
  T1              4                54
  T2              1                12
  T3+T4           5                28
                   vv
clus                N0 N1 N2
  5Q GAIN CNV        3  1  1
  5Q GAIN WILD-TYPE 17 11  3
D9V6, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  N0           3                17
  N1           1                11
  N2           1                 3
                   vv
clus                M0 M1 MX
  5Q GAIN CNV        5  1  3
  5Q GAIN WILD-TYPE 49  4 33
D9V7, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  M0           5                49
  M1           1                 4
  MX           3                33
                   vv
clus                 I II III IV
  5Q GAIN CNV        4  0   3  2
  5Q GAIN WILD-TYPE 49  7  21  7
D9V8, multiclass
     clus
vv    5Q GAIN CNV 5Q GAIN WILD-TYPE
  I             4                49
  II            0                 7
  III           3                21
  IV            2                 7

Clustering(10) Variable = 6p gain
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN CNV        2  2
  6P GAIN WILD-TYPE 81 12
      6P GAIN CNV 6P GAIN WILD-TYPE 
                4                93 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                12 
$`6P GAIN CNV`
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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         2.76       123.58        48.26        96.92 
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-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        15.48         5.85         5.26         6.84        32.12 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       41.33        11.05        30.51        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             7.89              0.03 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            93.34            182.73 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            11.62             14.07 
[1] "7.9 - 93.3 (11.6)"  "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6P GAIN WILD-TYPE" 
[1] "hr=" "3.6"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          0    4
  6P GAIN WILD-TYPE   34   66
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  FEMALE           0                34
  MALE             4                66
D10V4, continuous
[1] "Remove cluster labels:" "6P GAIN CNV"           
clus
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-7834 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  6P GAIN CNV        1  0     3
  6P GAIN WILD-TYPE 57 13    30
D10V5, multiclass
       clus
vv      6P GAIN CNV 6P GAIN WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           3                30
                   vv
clus                N0 N1 N2
  6P GAIN CNV        1  2  0
  6P GAIN WILD-TYPE 19 10  4
D10V6, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  N0           1                19
  N1           2                10
  N2           0                 4
                   vv
clus                M0 M1 MX
  6P GAIN CNV        2  2  0
  6P GAIN WILD-TYPE 52  3 36
D10V7, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  M0           2                52
  M1           2                 3
  MX           0                36
                   vv
clus                 I II III IV
  6P GAIN CNV        1  0   1  2
  6P GAIN WILD-TYPE 52  7  23  7
D10V8, multiclass
     clus
vv    6P GAIN CNV 6P GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           1                23
  IV            2                 7

Clustering(11) Variable = 6q gain
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN CNV        1  2
  6Q GAIN WILD-TYPE 82 12
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                94 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                12 
$`6Q GAIN CNV`
TCGA-AL-3466 TCGA-BQ-5893 TCGA-DW-5561 
        9.63         7.89        13.61 

$`6Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         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-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             7.89              0.03 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            13.61            182.73 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             9.63             14.35 
[1] "7.9 - 13.6 (9.6)"   "0.0 - 182.7 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"6Q GAIN WILD-TYPE" 
[1] "hr=" "19" 
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          0    3
  6Q GAIN WILD-TYPE   34   67
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  FEMALE           0                34
  MALE             3                67
D11V4, continuous
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-7834 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842        TCGA-EV-5901 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790        TCGA-G7-6793 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  6Q GAIN CNV        1  0     2
  6Q GAIN WILD-TYPE 57 13    31
D11V5, multiclass
       clus
vv      6Q GAIN CNV 6Q GAIN WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           2                31
                   vv
clus                N0 N1 N2
  6Q GAIN CNV        0  2  0
  6Q GAIN WILD-TYPE 20 10  4
D11V6, multiclass
[1] "Remove cluster labels:" "6Q GAIN CNV"           
clus
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                2                34 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3473 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268        TCGA-BQ-5877 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5894 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131        TCGA-G7-6789 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-J7-6720 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
                   vv
clus                M0 M1 MX
  6Q GAIN CNV        1  2  0
  6Q GAIN WILD-TYPE 53  3 36
D11V7, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  M0           1                53
  M1           2                 3
  MX           0                36
                   vv
clus                 I II III IV
  6Q GAIN CNV        1  0   0  2
  6Q GAIN WILD-TYPE 52  7  24  7
D11V8, multiclass
     clus
vv    6Q GAIN CNV 6Q GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           0                24
  IV            2                 7

Clustering(12) Variable = 7p gain
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV       47  4
  7P GAIN WILD-TYPE 36 10
      7P GAIN CNV 7P GAIN WILD-TYPE 
               51                46 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                4                10 
$`7P GAIN CNV`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-AL-3468 TCGA-AL-3471 
       15.95         0.03         0.89         1.61        53.79        13.55 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       30.31        44.61         3.58         5.88         4.83        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-B9-7268 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
        1.18        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-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 
       37.55        24.46         3.75        14.63         3.02        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.16        61.02        15.48         5.26         6.84        32.12 
TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-6846 
       30.51        14.07       182.73 

$`7P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.03         0.69         0.10        35.18         0.23         4.60 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 
        9.63        58.45        25.08        11.05         7.33         4.11 
TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        4.44         3.02        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
       22.92        43.17        21.63        40.83        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 
       13.25         7.63        11.97         7.89         2.76        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-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 
       13.74        79.82        54.87         5.85        41.33        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7966 
       34.82        12.72        14.63         3.68 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             0.03              0.03 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           182.73             93.34 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           13.610            14.185 
[1] "0.0 - 182.7 (13.6)" "0.0 - 93.3 (14.2)" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-GL-7966 
"7P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-GL-7966 
"7P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-GL-7966 
"7P GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV         13   42
  7P GAIN WILD-TYPE   21   28
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE          13                21
  MALE            42                28
D12V4, continuous
                   vv
clus                T1 T2 T3+T4
  7P GAIN CNV       38  8     9
  7P GAIN WILD-TYPE 20  5    24
D12V5, multiclass
       clus
vv      7P GAIN CNV 7P GAIN WILD-TYPE
  T1             38                20
  T2              8                 5
  T3+T4           9                24
                   vv
clus                N0 N1 N2
  7P GAIN CNV        7  2  2
  7P GAIN WILD-TYPE 13 10  2
D12V6, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  N0           7                13
  N1           2                10
  N2           2                 2
                   vv
clus                M0 M1 MX
  7P GAIN CNV       25  1 22
  7P GAIN WILD-TYPE 29  4 14
D12V7, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  M0          25                29
  M1           1                 4
  MX          22                14
                   vv
clus                 I II III IV
  7P GAIN CNV       36  2   5  4
  7P GAIN WILD-TYPE 17  5  19  5
D12V8, multiclass
     clus
vv    7P GAIN CNV 7P GAIN WILD-TYPE
  I            36                17
  II            2                 5
  III           5                19
  IV            4                 5

Clustering(13) Variable = 7q gain
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV       47  4
  7Q GAIN WILD-TYPE 36 10
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               51                46 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                4                10 
$`7Q GAIN CNV`
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-AL-3468 TCGA-AL-3471 
       15.95         0.03         0.89         1.61        53.79        13.55 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 
       30.31        44.61         3.58         5.88         4.83        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-B9-7268 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
        1.18        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-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 
       37.55        24.46         3.75        14.63         3.02        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.16        61.02        15.48         5.26         6.84        32.12 
TCGA-G7-6795 TCGA-G7-7502 TCGA-GL-6846 
       30.51        14.07       182.73 

$`7Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.03         0.69         0.10        35.18         0.23         4.60 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3926 
        9.63        58.45        25.08        11.05         7.33         4.11 
TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        4.44         3.02        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
       22.92        43.17        21.63        40.83        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 
       13.25         7.63        11.97         7.89         2.76        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-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6793 
       13.74        79.82        54.87         5.85        41.33        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7966 
       34.82        12.72        14.63         3.68 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             0.03              0.03 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
           182.73             93.34 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
           13.610            14.185 
[1] "0.0 - 182.7 (13.6)" "0.0 - 93.3 (14.2)" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-GL-7966 
"7Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-GL-7966 
"7Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-GL-7966 
"7Q GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV         14   42
  7Q GAIN WILD-TYPE   20   28
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE          14                20
  MALE            42                28
D13V4, continuous
                   vv
clus                T1 T2 T3+T4
  7Q GAIN CNV       38  8    10
  7Q GAIN WILD-TYPE 20  5    23
D13V5, multiclass
       clus
vv      7Q GAIN CNV 7Q GAIN WILD-TYPE
  T1             38                20
  T2              8                 5
  T3+T4          10                23
                   vv
clus                N0 N1 N2
  7Q GAIN CNV        7  2  2
  7Q GAIN WILD-TYPE 13 10  2
D13V6, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  N0           7                13
  N1           2                10
  N2           2                 2
                   vv
clus                M0 M1 MX
  7Q GAIN CNV       26  1 22
  7Q GAIN WILD-TYPE 28  4 14
D13V7, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0          26                28
  M1           1                 4
  MX          22                14
                   vv
clus                 I II III IV
  7Q GAIN CNV       36  2   6  4
  7Q GAIN WILD-TYPE 17  5  18  5
D13V8, multiclass
     clus
vv    7Q GAIN CNV 7Q GAIN WILD-TYPE
  I            36                17
  II            2                 5
  III           6                18
  IV            4                 5

Clustering(14) Variable = 8p gain
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV        4  1
  8P GAIN WILD-TYPE 79 13
      8P GAIN CNV 8P GAIN WILD-TYPE 
                5                92 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                1                13 
$`8P GAIN CNV`
TCGA-AL-3471 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-G7-6789 
       13.55        43.17        25.35        20.12         6.84 

$`8P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       53.79        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        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-7058 
       44.84        61.28        50.37        49.84        26.27        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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6792 
       54.87        15.48         5.85         5.26        32.12        41.33 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        30.51        34.82        12.72        14.63        14.07 
TCGA-GL-6846 TCGA-GL-7966 
      182.73         3.68 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             6.84              0.03 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            43.17            182.73 
      8P GAIN CNV 8P GAIN WILD-TYPE 
           20.120            13.675 
[1] "6.8 - 43.2 (20.1)"  "0.0 - 182.7 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8P GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          2    3
  8P GAIN WILD-TYPE   32   67
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE           2                32
  MALE             3                67
D14V4, continuous
                   vv
clus                T1 T2 T3+T4
  8P GAIN CNV        1  0     4
  8P GAIN WILD-TYPE 57 13    29
D14V5, multiclass
       clus
vv      8P GAIN CNV 8P GAIN WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  8P GAIN CNV        2  1  1
  8P GAIN WILD-TYPE 18 11  3
D14V6, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  N0           2                18
  N1           1                11
  N2           1                 3
                   vv
clus                M0 M1 MX
  8P GAIN CNV        4  0  1
  8P GAIN WILD-TYPE 50  5 35
D14V7, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  M0           4                50
  M1           0                 5
  MX           1                35
                   vv
clus                 I II III IV
  8P GAIN CNV        1  0   3  1
  8P GAIN WILD-TYPE 52  7  21  8
D14V8, multiclass
     clus
vv    8P GAIN CNV 8P GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           3                21
  IV            1                 8

Clustering(15) Variable = 8q gain
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV        4  3
  8Q GAIN WILD-TYPE 79 11
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                7                90 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                3                11 
$`8Q GAIN CNV`
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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
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-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-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        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-G7-6795 
       15.48         5.85         5.26        32.12        41.33        30.51 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       34.82        12.72        14.63        14.07       182.73         3.68 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             6.84              0.03 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            43.17            182.73 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
           13.550            13.905 
[1] "6.8 - 43.2 (13.6)"  "0.0 - 182.7 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8Q GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-GL-7966 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "5.8"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          3    4
  8Q GAIN WILD-TYPE   31   66
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE           3                31
  MALE             4                66
D15V4, continuous
[1] "Remove cluster labels:" "8Q GAIN CNV"           
clus
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                20 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-DW-5560        TCGA-DW-5561 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  8Q GAIN CNV        1  0     6
  8Q GAIN WILD-TYPE 57 13    27
D15V5, multiclass
       clus
vv      8Q GAIN CNV 8Q GAIN WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           6                27
                   vv
clus                N0 N1 N2
  8Q GAIN CNV        2  2  2
  8Q GAIN WILD-TYPE 18 10  2
D15V6, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  N0           2                18
  N1           2                10
  N2           2                 2
                   vv
clus                M0 M1 MX
  8Q GAIN CNV        4  1  2
  8Q GAIN WILD-TYPE 50  4 34
D15V7, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0           4                50
  M1           1                 4
  MX           2                34
                   vv
clus                 I II III IV
  8Q GAIN CNV        1  0   3  3
  8Q GAIN WILD-TYPE 52  7  21  6
D15V8, multiclass
     clus
vv    8Q GAIN CNV 8Q GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           3                21
  IV            3                 6

Clustering(16) Variable = 10p gain
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN CNV        3  0
  10P GAIN WILD-TYPE 80 14
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 3                 94 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 0                 14 
$`10P GAIN CNV`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 
        4.60        53.79         1.08 

$`10P GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
        0.89         0.23         1.61         9.63        58.45        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       10.82         3.02         0.46         0.62         6.44         1.18 
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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      10P GAIN CNV 10P GAIN WILD-TYPE 
              1.08               0.03 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             53.79             182.73 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             4.600             13.905 
[1] "1.1 - 53.8 (4.6)"   "0.0 - 182.7 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"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-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"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-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"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-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10P GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          1    3
  10P GAIN WILD-TYPE   33   67
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  FEMALE            1                 33
  MALE              3                 67
D16V4, continuous
                    vv
clus                 T1 T2 T3+T4
  10P GAIN CNV        2  1     1
  10P GAIN WILD-TYPE 56 12    32
D16V5, multiclass
       clus
vv      10P GAIN CNV 10P GAIN WILD-TYPE
  T1               2                 56
  T2               1                 12
  T3+T4            1                 32
                    vv
clus                 N0 N1 N2
  10P GAIN CNV        0  0  0
  10P GAIN WILD-TYPE 20 12  4
D16V6, multiclass
                    vv
clus                 M0 M1 MX
  10P GAIN CNV        2  0  1
  10P GAIN WILD-TYPE 52  5 35
D16V7, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  M0            2                 52
  M1            0                  5
  MX            1                 35
                    vv
clus                  I II III IV
  10P GAIN CNV        1  0   1  0
  10P GAIN WILD-TYPE 52  7  23  9
D16V8, multiclass
[1] "Remove cluster labels:" "10P GAIN CNV"          
clus
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 2                 91 
        TCGA-A4-7287         TCGA-A4-7583         TCGA-A4-7584 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7828 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-AL-3466 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3473         TCGA-AL-7173 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4115 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-7268         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-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         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-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-HE-7128         TCGA-HE-7129 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-J7-6720 
"10P GAIN WILD-TYPE" 

Clustering(17) Variable = 10q gain
D17V1, survival
                    sevent
clus2                 0  1
  10Q GAIN CNV        3  0
  10Q GAIN WILD-TYPE 80 14
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 3                 94 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 0                 14 
$`10Q GAIN CNV`
TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 
        4.60        53.79         1.08 

$`10Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
        0.89         0.23         1.61         9.63        58.45        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        50.50         0.69 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       10.82         3.02         0.46         0.62         6.44         1.18 
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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      10Q GAIN CNV 10Q GAIN WILD-TYPE 
              1.08               0.03 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
             53.79             182.73 
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
             4.600             13.905 
[1] "1.1 - 53.8 (4.6)"   "0.0 - 182.7 (13.9)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "10Q GAIN CNV" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE"       "10Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"10Q GAIN WILD-TYPE" 
[1] "hr="     "2.6e+07"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN CNV          0    3
  10Q GAIN WILD-TYPE   34   67
        clus
vv       10Q GAIN CNV 10Q GAIN WILD-TYPE
  FEMALE            0                 34
  MALE              3                 67
D17V4, continuous
                    vv
clus                 T1 T2 T3+T4
  10Q GAIN CNV        2  1     0
  10Q GAIN WILD-TYPE 56 12    33
D17V5, multiclass
       clus
vv      10Q GAIN CNV 10Q GAIN WILD-TYPE
  T1               2                 56
  T2               1                 12
  T3+T4            0                 33
                    vv
clus                 N0 N1 N2
  10Q GAIN CNV        0  0  0
  10Q GAIN WILD-TYPE 20 12  4
D17V6, multiclass
                    vv
clus                 M0 M1 MX
  10Q GAIN CNV        1  0  1
  10Q GAIN WILD-TYPE 53  5 35
D17V7, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 2                 93 
        TCGA-A4-7287         TCGA-A4-7288         TCGA-A4-7583 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7996         TCGA-AL-3466         TCGA-AL-3467 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-7332 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-HE-7128 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130         TCGA-J7-6720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                  I II III IV
  10Q GAIN CNV        1  0   0  0
  10Q GAIN WILD-TYPE 52  7  24  9
D17V8, multiclass
[1] "Remove cluster labels:" "10Q GAIN CNV"          
clus
      10Q GAIN CNV 10Q GAIN WILD-TYPE 
                 1                 92 
        TCGA-A4-7287         TCGA-A4-7583         TCGA-A4-7584 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7828 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-AL-3466 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3473         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4115 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-7268         TCGA-BQ-5875 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7502         TCGA-GL-6846         TCGA-GL-7773 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-HE-7128         TCGA-HE-7129 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-7130         TCGA-J7-6720 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 

Clustering(18) Variable = 12p gain
D18V1, survival
                    sevent
clus2                 0  1
  12P GAIN CNV       25  4
  12P GAIN WILD-TYPE 58 10
      12P GAIN CNV 12P GAIN WILD-TYPE 
                29                 68 
      12P GAIN CNV 12P GAIN WILD-TYPE 
                 4                 10 
$`12P GAIN CNV`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-8098 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 
        0.03         0.03         4.60        53.79        13.55        44.61 
TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
        3.58        50.50         0.69         1.08         6.44         1.18 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7059 TCGA-BQ-7061 
        8.84        43.17        25.35         0.95         7.63         7.13 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6132 
        3.78        13.61        37.55         3.75        14.63        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-G7-6789 TCGA-G7-6795 TCGA-GL-6846 
       51.16        61.02         6.84        30.51       182.73 

$`12P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
        1.61         9.63        58.45        30.31        25.08        11.05 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
        7.33         4.11         5.88         4.44         4.83        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        3.02         0.46         0.62        86.73        19.23        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        13.25        10.82         7.63        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-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 
        7.00        11.61       129.86        35.93        24.46        13.74 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        3.02        79.82        54.87        15.48         5.85         5.26 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       32.12        41.33        11.05        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

      12P GAIN CNV 12P GAIN WILD-TYPE 
              0.03               0.10 
      12P GAIN CNV 12P GAIN WILD-TYPE 
            182.73             129.86 
      12P GAIN CNV 12P GAIN WILD-TYPE 
             8.840             15.055 
[1] "0.0 - 182.7 (8.8)"  "0.1 - 129.9 (15.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-GL-7966 
"12P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-GL-7966 
"12P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12P GAIN WILD-TYPE"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12P GAIN CNV"       "12P GAIN CNV" "12P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12P GAIN WILD-TYPE"       "12P GAIN CNV"       "12P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12P GAIN CNV" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"       "12P GAIN CNV" 
        TCGA-GL-7966 
"12P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN CNV          5   26
  12P GAIN WILD-TYPE   29   44
        clus
vv       12P GAIN CNV 12P GAIN WILD-TYPE
  FEMALE            5                 29
  MALE             26                 44
D18V4, continuous
                    vv
clus                 T1 T2 T3+T4
  12P GAIN CNV       18  4     9
  12P GAIN WILD-TYPE 40  9    24
D18V5, multiclass
       clus
vv      12P GAIN CNV 12P GAIN WILD-TYPE
  T1              18                 40
  T2               4                  9
  T3+T4            9                 24
                    vv
clus                 N0 N1 N2
  12P GAIN CNV        4  3  2
  12P GAIN WILD-TYPE 16  9  2
D18V6, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  N0            4                 16
  N1            3                  9
  N2            2                  2
                    vv
clus                 M0 M1 MX
  12P GAIN CNV       12  1 13
  12P GAIN WILD-TYPE 42  4 23
D18V7, multiclass
    clus
vv   12P GAIN CNV 12P GAIN WILD-TYPE
  M0           12                 42
  M1            1                  4
  MX           13                 23
                    vv
clus                  I II III IV
  12P GAIN CNV       16  1   4  4
  12P GAIN WILD-TYPE 37  6  20  5
D18V8, multiclass
     clus
vv    12P GAIN CNV 12P GAIN WILD-TYPE
  I             16                 37
  II             1                  6
  III            4                 20
  IV             4                  5

Clustering(19) Variable = 12q gain
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN CNV       25  4
  12Q GAIN WILD-TYPE 58 10
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                29                 68 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 4                 10 
$`12Q GAIN CNV`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-8098 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 
        0.03         0.03         4.60        53.79        13.55        44.61 
TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
        3.58        50.50         0.69         1.08         6.44         1.18 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7059 TCGA-BQ-7061 
        8.84        43.17        25.35         0.95         7.63         7.13 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6132 
        3.78        13.61        37.55         3.75        14.63        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-G7-6789 TCGA-G7-6795 TCGA-GL-6846 
       51.16        61.02         6.84        30.51       182.73 

$`12Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-B1-5398 
        1.61         9.63        58.45        30.31        25.08        11.05 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
        7.33         4.11         5.88         4.44         4.83        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        3.02         0.46         0.62        86.73        19.23        63.72 
TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        13.25        10.82         7.63        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-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 
        7.00        11.61       129.86        35.93        24.46        13.74 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        3.02        79.82        54.87        15.48         5.85         5.26 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       32.12        41.33        11.05        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              0.03               0.10 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
            182.73             129.86 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             8.840             15.055 
[1] "0.0 - 182.7 (8.8)"  "0.1 - 129.9 (15.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-GL-7966 
"12Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-GL-7966 
"12Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "12Q GAIN CNV"       "12Q GAIN CNV" "12Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"12Q GAIN WILD-TYPE"       "12Q GAIN CNV"       "12Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "12Q GAIN CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"       "12Q GAIN CNV" 
        TCGA-GL-7966 
"12Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          5   26
  12Q GAIN WILD-TYPE   29   44
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  FEMALE            5                 29
  MALE             26                 44
D19V4, continuous
                    vv
clus                 T1 T2 T3+T4
  12Q GAIN CNV       18  4     9
  12Q GAIN WILD-TYPE 40  9    24
D19V5, multiclass
       clus
vv      12Q GAIN CNV 12Q GAIN WILD-TYPE
  T1              18                 40
  T2               4                  9
  T3+T4            9                 24
                    vv
clus                 N0 N1 N2
  12Q GAIN CNV        4  3  2
  12Q GAIN WILD-TYPE 16  9  2
D19V6, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  N0            4                 16
  N1            3                  9
  N2            2                  2
                    vv
clus                 M0 M1 MX
  12Q GAIN CNV       12  1 13
  12Q GAIN WILD-TYPE 42  4 23
D19V7, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0           12                 42
  M1            1                  4
  MX           13                 23
                    vv
clus                  I II III IV
  12Q GAIN CNV       16  1   4  4
  12Q GAIN WILD-TYPE 37  6  20  5
D19V8, multiclass
     clus
vv    12Q GAIN CNV 12Q GAIN WILD-TYPE
  I             16                 37
  II             1                  6
  III            4                 20
  IV             4                  5

Clustering(20) Variable = 13q gain
D20V1, survival
                    sevent
clus2                 0  1
  13Q GAIN CNV        9  1
  13Q GAIN WILD-TYPE 74 13
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                10                 87 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                 13 
$`13Q GAIN CNV`
TCGA-B1-5398 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-7046 TCGA-DW-5561 
       11.05         4.83         0.46         1.08        96.92        13.61 
TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6796 
       51.16         5.26        32.12        34.82 

$`13Q GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 
       53.79        13.55        30.31        25.08        44.61         7.33 
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-B9-7268 TCGA-BQ-5875 
       10.82         3.02         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.58        48.26        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-7834 TCGA-DW-7836 
        7.00         7.13         3.78        11.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.82        80.84        61.02        54.87        15.48         5.85 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 
        6.84        41.33        11.05        30.51        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      13Q GAIN CNV 13Q GAIN WILD-TYPE 
              0.46               0.03 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
             96.92             182.73 
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
             12.33              14.07 
[1] "0.5 - 96.9 (12.3)"  "0.0 - 182.7 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"13Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"13Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV"       "13Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE"       "13Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "13Q GAIN CNV" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q GAIN WILD-TYPE"       "13Q GAIN CNV" "13Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"13Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN CNV          4    7
  13Q GAIN WILD-TYPE   30   63
        clus
vv       13Q GAIN CNV 13Q GAIN WILD-TYPE
  FEMALE            4                 30
  MALE              7                 63
D20V4, continuous
                    vv
clus                 T1 T2 T3+T4
  13Q GAIN CNV        8  1     2
  13Q GAIN WILD-TYPE 50 12    31
D20V5, multiclass
       clus
vv      13Q GAIN CNV 13Q GAIN WILD-TYPE
  T1               8                 50
  T2               1                 12
  T3+T4            2                 31
                    vv
clus                 N0 N1 N2
  13Q GAIN CNV        1  0  0
  13Q GAIN WILD-TYPE 19 12  4
D20V6, multiclass
[1] "Remove cluster labels:" "13Q GAIN CNV"          
clus
      13Q GAIN CNV 13Q GAIN WILD-TYPE 
                 1                 35 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3473         TCGA-AL-7173 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-5885         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-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-J7-6720 
"13Q GAIN WILD-TYPE" "13Q GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  13Q GAIN CNV        5  0  4
  13Q GAIN WILD-TYPE 49  5 32
D20V7, multiclass
    clus
vv   13Q GAIN CNV 13Q GAIN WILD-TYPE
  M0            5                 49
  M1            0                  5
  MX            4                 32
                    vv
clus                  I II III IV
  13Q GAIN CNV        7  0   2  0
  13Q GAIN WILD-TYPE 46  7  22  9
D20V8, multiclass
     clus
vv    13Q GAIN CNV 13Q GAIN WILD-TYPE
  I              7                 46
  II             0                  7
  III            2                 22
  IV             0                  9

Clustering(21) Variable = 16p gain
D21V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV       36  5
  16P GAIN WILD-TYPE 47  9
      16P GAIN CNV 16P GAIN WILD-TYPE 
                41                 56 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 5                  9 
$`16P GAIN CNV`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-AL-3466 
        0.03        15.95         0.10        35.18         1.61         9.63 
TCGA-AL-3468 TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 
       53.79        13.55        11.05         5.88         4.83         0.69 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 
       47.80        26.04        25.35         7.63         0.95       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-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 
      129.86        35.93        24.46        51.16        61.02         5.85 
TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6797 TCGA-GL-6846 
        5.26         6.84        32.12        12.72       182.73 

$`16P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3467 
        0.69         0.03         0.89         0.23         4.60        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61         7.33         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-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        13.25        10.82        11.97         7.89         2.76 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       93.34        44.84        61.28        49.84        26.27        20.12 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 
        7.63         7.13        11.61        13.61        37.55        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 
        3.75        14.63         3.02        79.82        80.84        54.87 
TCGA-EV-5901 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       15.48        41.33        11.05        30.51        34.82        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              0.03               0.03 
      16P GAIN CNV 16P GAIN WILD-TYPE 
            182.73              93.34 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             11.28              14.63 
[1] "0.0 - 182.7 (11.3)" "0.0 - 93.3 (14.6)" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-GL-7966 
"16P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-GL-7966 
"16P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16P GAIN CNV"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "16P GAIN CNV" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16P GAIN WILD-TYPE"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16P GAIN CNV"       "16P GAIN CNV"       "16P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"       "16P GAIN CNV" 
        TCGA-GL-7966 
"16P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          8   36
  16P GAIN WILD-TYPE   26   34
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE            8                 26
  MALE             36                 34
D21V4, continuous
                    vv
clus                 T1 T2 T3+T4
  16P GAIN CNV       24  6    14
  16P GAIN WILD-TYPE 34  7    19
D21V5, multiclass
       clus
vv      16P GAIN CNV 16P GAIN WILD-TYPE
  T1              24                 34
  T2               6                  7
  T3+T4           14                 19
                    vv
clus                 N0 N1 N2
  16P GAIN CNV        9  2  2
  16P GAIN WILD-TYPE 11 10  2
D21V6, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  N0            9                 11
  N1            2                 10
  N2            2                  2
                    vv
clus                 M0 M1 MX
  16P GAIN CNV       23  1 14
  16P GAIN WILD-TYPE 31  4 22
D21V7, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  M0           23                 31
  M1            1                  4
  MX           14                 22
                    vv
clus                  I II III IV
  16P GAIN CNV       21  2  11  3
  16P GAIN WILD-TYPE 32  5  13  6
D21V8, multiclass
     clus
vv    16P GAIN CNV 16P GAIN WILD-TYPE
  I             21                 32
  II             2                  5
  III           11                 13
  IV             3                  6

Clustering(22) Variable = 16q gain
D22V1, survival
                    sevent
clus2                 0  1
  16Q GAIN CNV       35  3
  16Q GAIN WILD-TYPE 48 11
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                38                 59 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
                 3                 11 
$`16Q GAIN CNV`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-AL-3468 
        0.03        15.95         0.10        35.18         1.61        53.79 
TCGA-AL-3471 TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 
       13.55        11.05         5.88         4.83         0.69         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5881 
        1.08         0.62         6.44         1.18        86.73        47.80 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       26.04        25.35         0.95       123.58        48.26        96.92 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       50.37         7.00         3.78       129.86        35.93        24.46 
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 

$`16Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3466 
        0.69         0.03         0.89         0.23         4.60         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 
       58.45        30.31        25.08        44.61         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-BQ-5876 
        4.11         4.44        50.50        10.82         3.02        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       26.04        30.28        13.25        10.82         7.63        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
        7.89         2.76        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
       26.27        20.12        11.28         7.63         7.13        11.61 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       13.61        37.55        13.74         3.75        14.63         3.02 
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 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       30.51        34.82        14.63        14.07         3.68 

      16Q GAIN CNV 16Q GAIN WILD-TYPE 
              0.03               0.03 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
            182.73              93.34 
      16Q GAIN CNV 16Q GAIN WILD-TYPE 
            13.135             14.070 
[1] "0.0 - 182.7 (13.1)" "0.0 - 93.3 (14.1)" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-GL-7966 
"16Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-GL-7966 
"16Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "16Q GAIN CNV"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q GAIN WILD-TYPE"       "16Q GAIN CNV" "16Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "16Q GAIN CNV"       "16Q GAIN CNV"       "16Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "16Q GAIN CNV" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"       "16Q GAIN CNV" 
        TCGA-GL-7966 
"16Q GAIN WILD-TYPE" 
[1] "hr=" "2.8"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN CNV          8   33
  16Q GAIN WILD-TYPE   26   37
        clus
vv       16Q GAIN CNV 16Q GAIN WILD-TYPE
  FEMALE            8                 26
  MALE             33                 37
D22V4, continuous
                    vv
clus                 T1 T2 T3+T4
  16Q GAIN CNV       24  6    11
  16Q GAIN WILD-TYPE 34  7    22
D22V5, multiclass
       clus
vv      16Q GAIN CNV 16Q GAIN WILD-TYPE
  T1              24                 34
  T2               6                  7
  T3+T4           11                 22
                    vv
clus                 N0 N1 N2
  16Q GAIN CNV        8  1  1
  16Q GAIN WILD-TYPE 12 11  3
D22V6, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  N0            8                 12
  N1            1                 11
  N2            1                  3
                    vv
clus                 M0 M1 MX
  16Q GAIN CNV       21  0 14
  16Q GAIN WILD-TYPE 33  5 22
D22V7, multiclass
    clus
vv   16Q GAIN CNV 16Q GAIN WILD-TYPE
  M0           21                 33
  M1            0                  5
  MX           14                 22
                    vv
clus                  I II III IV
  16Q GAIN CNV       21  2   9  2
  16Q GAIN WILD-TYPE 32  5  15  7
D22V8, multiclass
     clus
vv    16Q GAIN CNV 16Q GAIN WILD-TYPE
  I             21                 32
  II             2                  5
  III            9                 15
  IV             2                  7

Clustering(23) Variable = 17p gain
D23V1, survival
                    sevent
clus2                 0  1
  17P GAIN CNV       44  4
  17P GAIN WILD-TYPE 39 10
      17P GAIN CNV 17P GAIN WILD-TYPE 
                48                 49 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 4                 10 
$`17P GAIN CNV`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-AL-3468 
        0.03        15.95         0.03         0.89         1.61        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
       13.55        30.31         7.33         3.58         5.88         4.83 
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-B9-7268 TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 
        6.44         1.18        47.80        25.35         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 
        7.89        48.26        96.92        50.37         7.00         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6134 
       13.74         3.75        14.63         3.02        51.16        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
       15.48         5.26        32.12        30.51        34.82       182.73 

$`17P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-AL-3466 
        0.69         0.10        35.18         0.23         4.60         9.63 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 
       58.45        25.08        44.61        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-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        21.63        40.83        26.04        30.28        26.04 
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 TCGA-G7-7501 TCGA-G7-7502 
        6.84        41.33        11.05        12.72        14.63        14.07 
TCGA-GL-7966 
        3.68 

      17P GAIN CNV 17P GAIN WILD-TYPE 
              0.03               0.10 
      17P GAIN CNV 17P GAIN WILD-TYPE 
            182.73             123.58 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             12.76              19.23 
[1] "0.0 - 182.7 (12.8)" "0.1 - 123.6 (19.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-GL-7966 
"17P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-GL-7966 
"17P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17P GAIN WILD-TYPE"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17P GAIN CNV"       "17P GAIN CNV"       "17P GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17P GAIN CNV"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-GL-7966 
"17P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV         11   41
  17P GAIN WILD-TYPE   23   29
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  FEMALE           11                 23
  MALE             41                 29
D23V4, continuous
                    vv
clus                 T1 T2 T3+T4
  17P GAIN CNV       36  9     7
  17P GAIN WILD-TYPE 22  4    26
D23V5, multiclass
       clus
vv      17P GAIN CNV 17P GAIN WILD-TYPE
  T1              36                 22
  T2               9                  4
  T3+T4            7                 26
                    vv
clus                 N0 N1 N2
  17P GAIN CNV        8  2  0
  17P GAIN WILD-TYPE 12 10  4
D23V6, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  N0            8                 12
  N1            2                 10
  N2            0                  4
                    vv
clus                 M0 M1 MX
  17P GAIN CNV       21  1 22
  17P GAIN WILD-TYPE 33  4 14
D23V7, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  M0           21                 33
  M1            1                  4
  MX           22                 14
                    vv
clus                  I II III IV
  17P GAIN CNV       34  3   4  2
  17P GAIN WILD-TYPE 19  4  20  7
D23V8, multiclass
     clus
vv    17P GAIN CNV 17P GAIN WILD-TYPE
  I             34                 19
  II             3                  4
  III            4                 20
  IV             2                  7

Clustering(24) Variable = 17q gain
D24V1, survival
                    sevent
clus2                 0  1
  17Q GAIN CNV       51  7
  17Q GAIN WILD-TYPE 32  7
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                58                 39 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 7                  7 
$`17Q GAIN CNV`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.03        15.95         0.03         0.89         0.23         1.61 
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-B1-7332 TCGA-B3-3925 
        9.63        53.79        13.55        30.31         7.33         3.58 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
        5.88         4.83        50.50         0.69        10.82         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5881 
        1.08         0.62         6.44         1.18        86.73        47.80 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        13.25         7.63         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 
        7.89        48.26        96.92        50.37        49.84        11.28 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.00         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       51.16        61.02        15.48         5.26         6.84        32.12 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
       11.05        30.51        34.82       182.73 

$`17Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3473 
        0.69         0.10        35.18         4.60        58.45        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-BQ-5876 
       44.61        11.05         4.11         4.44         3.02        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.84        63.72        22.92        43.17        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
       26.04        30.28        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-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-G7-6792 TCGA-G7-6797 
       79.82        80.84        54.87         5.85        41.33        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
       14.63        14.07         3.68 

      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              0.03               0.10 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
            182.73             123.58 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             11.79              21.63 
[1] "0.0 - 182.7 (11.8)" "0.1 - 123.6 (21.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-GL-7966 
"17Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-GL-7966 
"17Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "17Q GAIN CNV"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV"       "17Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-GL-7966 
"17Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV         17   45
  17Q GAIN WILD-TYPE   17   25
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  FEMALE           17                 17
  MALE             45                 25
D24V4, continuous
                    vv
clus                 T1 T2 T3+T4
  17Q GAIN CNV       37 10    15
  17Q GAIN WILD-TYPE 21  3    18
D24V5, multiclass
       clus
vv      17Q GAIN CNV 17Q GAIN WILD-TYPE
  T1              37                 21
  T2              10                  3
  T3+T4           15                 18
                    vv
clus                 N0 N1 N2
  17Q GAIN CNV       11  3  3
  17Q GAIN WILD-TYPE  9  9  1
D24V6, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  N0           11                  9
  N1            3                  9
  N2            3                  1
                    vv
clus                 M0 M1 MX
  17Q GAIN CNV       27  2 25
  17Q GAIN WILD-TYPE 27  3 11
D24V7, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  M0           27                 27
  M1            2                  3
  MX           25                 11
                    vv
clus                  I II III IV
  17Q GAIN CNV       35  4   9  5
  17Q GAIN WILD-TYPE 18  3  15  4
D24V8, multiclass
     clus
vv    17Q GAIN CNV 17Q GAIN WILD-TYPE
  I             35                 18
  II             4                  3
  III            9                 15
  IV             5                  4

Clustering(25) Variable = 18p gain
D25V1, survival
                    sevent
clus2                 0  1
  18P GAIN CNV        5  1
  18P GAIN WILD-TYPE 78 13
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 6                 91 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 13 
$`18P GAIN CNV`
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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        3.58         4.11         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        3.02         0.46         1.08         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-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-DW-7834 
        7.63         7.00         7.13         3.78        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        79.82        80.84        51.16        61.02        54.87 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       15.48         5.85         5.26         6.84        41.33        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       30.51        34.82        12.72        14.63        14.07       182.73 
TCGA-GL-7966 
        3.68 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              0.62               0.03 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             32.12             182.73 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             7.755             14.630 
[1] "0.6 - 32.1 (7.8)"   "0.0 - 182.7 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"       "18P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18P GAIN WILD-TYPE" 
[1] "hr=" "3.7"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    5
  18P GAIN WILD-TYPE   33   65
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            1                 33
  MALE              5                 65
D25V4, continuous
                    vv
clus                 T1 T2 T3+T4
  18P GAIN CNV        3  1     2
  18P GAIN WILD-TYPE 55 12    31
D25V5, multiclass
       clus
vv      18P GAIN CNV 18P GAIN WILD-TYPE
  T1               3                 55
  T2               1                 12
  T3+T4            2                 31
                    vv
clus                 N0 N1 N2
  18P GAIN CNV        0  1  0
  18P GAIN WILD-TYPE 20 11  4
D25V6, multiclass
[1] "Remove cluster labels:" "18P GAIN CNV"          
clus
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 35 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-5885         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-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-G7-6789         TCGA-G7-6793 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-GL-7966         TCGA-J7-6720 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  18P GAIN CNV        3  1  1
  18P GAIN WILD-TYPE 51  4 35
D25V7, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  M0            3                 51
  M1            1                  4
  MX            1                 35
                    vv
clus                  I II III IV
  18P GAIN CNV        3  1   1  1
  18P GAIN WILD-TYPE 50  6  23  8
D25V8, multiclass
     clus
vv    18P GAIN CNV 18P GAIN WILD-TYPE
  I              3                 50
  II             1                  6
  III            1                 23
  IV             1                  8

Clustering(26) Variable = 18q gain
D26V1, survival
                    sevent
clus2                 0  1
  18Q GAIN CNV        4  0
  18Q GAIN WILD-TYPE 79 14
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 93 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 0                 14 
$`18Q GAIN CNV`
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-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        7.33         3.58         4.11         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
        0.69        10.82         3.02         0.46         1.08         6.44 
TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       41.33        11.05        30.51        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              0.62               0.03 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             32.12             182.73 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             8.745             14.070 
[1] "0.6 - 32.1 (8.7)"   "0.0 - 182.7 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE"       "18Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"18Q GAIN WILD-TYPE" 
[1] "hr="     "9400000"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    3
  18Q GAIN WILD-TYPE   33   67
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            1                 33
  MALE              3                 67
D26V4, continuous
[1] "Remove cluster labels:" "18Q GAIN CNV"          
clus
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6796         TCGA-G7-6797 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  18Q GAIN CNV        3  0     1
  18Q GAIN WILD-TYPE 55 13    32
D26V5, multiclass
       clus
vv      18Q GAIN CNV 18Q GAIN WILD-TYPE
  T1               3                 55
  T2               0                 13
  T3+T4            1                 32
                    vv
clus                 N0 N1 N2
  18Q GAIN CNV        0  0  0
  18Q GAIN WILD-TYPE 20 12  4
D26V6, multiclass
                    vv
clus                 M0 M1 MX
  18Q GAIN CNV        2  0  1
  18Q GAIN WILD-TYPE 52  5 35
D26V7, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0            2                 52
  M1            0                  5
  MX            1                 35
                    vv
clus                  I II III IV
  18Q GAIN CNV        3  0   1  0
  18Q GAIN WILD-TYPE 50  7  23  9
D26V8, multiclass
     clus
vv    18Q GAIN CNV 18Q GAIN WILD-TYPE
  I              3                 50
  II             0                  7
  III            1                 23
  IV             0                  9

Clustering(27) Variable = 20p gain
D27V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV       28  2
  20P GAIN WILD-TYPE 55 12
      20P GAIN CNV 20P GAIN WILD-TYPE 
                30                 67 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 2                 12 
$`20P GAIN CNV`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3468 
        0.03         0.03         0.89         1.61         9.63        53.79 
TCGA-AL-3471 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4117 
       13.55         7.33         3.58         5.88         4.83         0.46 
TCGA-B9-4617 TCGA-B9-7268 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7046 
        1.08         1.18        25.35         0.95         2.76        96.92 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       50.37         3.78        11.61        13.61        35.93        14.63 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 
       80.84        51.16         5.85         6.84        30.51        12.72 

$`20P GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.69        15.95         0.10        35.18         0.23         4.60 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3926 
       58.45        30.31        25.08        44.61        11.05         4.11 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 
        4.44        50.50         0.69        10.82         3.02         0.62 
TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        6.44        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        13.25        10.82         7.63        11.97         7.89 
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-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
      129.86        37.55        24.46        13.74         3.75         3.02 
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-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       41.33        11.05        34.82        14.63        14.07       182.73 
TCGA-GL-7966 
        3.68 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.03               0.10 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             96.92             182.73 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             7.085             20.120 
[1] "0.0 - 96.9 (7.1)"   "0.1 - 182.7 (20.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20P GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20P GAIN CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          9   22
  20P GAIN WILD-TYPE   25   48
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE            9                 25
  MALE             22                 48
D27V4, continuous
                    vv
clus                 T1 T2 T3+T4
  20P GAIN CNV       18  6     7
  20P GAIN WILD-TYPE 40  7    26
D27V5, multiclass
       clus
vv      20P GAIN CNV 20P GAIN WILD-TYPE
  T1              18                 40
  T2               6                  7
  T3+T4            7                 26
                    vv
clus                 N0 N1 N2
  20P GAIN CNV        5  2  1
  20P GAIN WILD-TYPE 15 10  3
D27V6, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  N0            5                 15
  N1            2                 10
  N2            1                  3
                    vv
clus                 M0 M1 MX
  20P GAIN CNV       13  2 13
  20P GAIN WILD-TYPE 41  3 23
D27V7, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  M0           13                 41
  M1            2                  3
  MX           13                 23
                    vv
clus                  I II III IV
  20P GAIN CNV       16  3   4  3
  20P GAIN WILD-TYPE 37  4  20  6
D27V8, multiclass
     clus
vv    20P GAIN CNV 20P GAIN WILD-TYPE
  I             16                 37
  II             3                  4
  III            4                 20
  IV             3                  6

Clustering(28) Variable = 20q gain
D28V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV       28  2
  20Q GAIN WILD-TYPE 55 12
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                30                 67 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 2                 12 
$`20Q GAIN CNV`
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3468 
        0.03         0.03         0.89         1.61         9.63        53.79 
TCGA-AL-3471 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 
       13.55         3.58         5.88         4.44         4.83         0.46 
TCGA-B9-4617 TCGA-B9-7268 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7046 
        1.08         1.18        25.35         0.95         2.76        96.92 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       50.37         3.78        11.61        13.61        35.93        14.63 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 
       80.84        51.16         5.85         6.84        30.51        12.72 

$`20Q GAIN WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
        0.69        15.95         0.10        35.18         0.23         4.60 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       58.45        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3926 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 
        4.11        50.50         0.69        10.82         3.02         0.62 
TCGA-B9-5156 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        6.44        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        13.25        10.82         7.63        11.97         7.89 
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-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
      129.86        37.55        24.46        13.74         3.75         3.02 
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-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       41.33        11.05        34.82        14.63        14.07       182.73 
TCGA-GL-7966 
        3.68 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.03               0.10 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             96.92             182.73 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              6.36              20.12 
[1] "0.0 - 96.9 (6.4)"   "0.1 - 182.7 (20.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20Q GAIN WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "20Q GAIN CNV"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-GL-7966 
"20Q GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          9   23
  20Q GAIN WILD-TYPE   25   47
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE            9                 25
  MALE             23                 47
D28V4, continuous
                    vv
clus                 T1 T2 T3+T4
  20Q GAIN CNV       18  6     8
  20Q GAIN WILD-TYPE 40  7    25
D28V5, multiclass
       clus
vv      20Q GAIN CNV 20Q GAIN WILD-TYPE
  T1              18                 40
  T2               6                  7
  T3+T4            8                 25
                    vv
clus                 N0 N1 N2
  20Q GAIN CNV        5  2  1
  20Q GAIN WILD-TYPE 15 10  3
D28V6, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  N0            5                 15
  N1            2                 10
  N2            1                  3
                    vv
clus                 M0 M1 MX
  20Q GAIN CNV       15  2 12
  20Q GAIN WILD-TYPE 39  3 24
D28V7, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  M0           15                 39
  M1            2                  3
  MX           12                 24
                    vv
clus                  I II III IV
  20Q GAIN CNV       16  3   5  3
  20Q GAIN WILD-TYPE 37  4  19  6
D28V8, multiclass
     clus
vv    20Q GAIN CNV 20Q GAIN WILD-TYPE
  I             16                 37
  II             3                  4
  III            5                 19
  IV             3                  6

Clustering(29) Variable = Xq gain
D29V1, survival
                   sevent
clus2                0  1
  XQ GAIN CNV        3  1
  XQ GAIN WILD-TYPE 80 13
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4                93 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                1                13 
$`XQ GAIN CNV`
TCGA-B9-4617 TCGA-BQ-5891 TCGA-DZ-6133 TCGA-G7-6789 
        1.08         0.95        51.16         6.84 

$`XQ GAIN WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33         3.58         4.11         5.88         4.44         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       50.50         0.69        10.82         3.02         0.46         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-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-G7-7501 
       41.33        11.05        30.51        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      XQ GAIN CNV XQ GAIN WILD-TYPE 
             0.95              0.03 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            51.16            182.73 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
             3.96             14.07 
[1] "0.9 - 51.2 (4.0)"   "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GL-7966 
"XQ GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GL-7966 
"XQ GAIN WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GL-7966 
"XQ GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          3    1
  XQ GAIN WILD-TYPE   31   69
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  FEMALE           3                31
  MALE             1                69
D29V4, continuous
                   vv
clus                T1 T2 T3+T4
  XQ GAIN CNV        2  0     2
  XQ GAIN WILD-TYPE 56 13    31
D29V5, multiclass
       clus
vv      XQ GAIN CNV XQ GAIN WILD-TYPE
  T1              2                56
  T2              0                13
  T3+T4           2                31
                   vv
clus                N0 N1 N2
  XQ GAIN CNV        1  0  1
  XQ GAIN WILD-TYPE 19 12  3
D29V6, multiclass
[1] "Remove cluster labels:" "XQ GAIN CNV"           
clus
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                2                34 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3466 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5889        TCGA-BQ-5890        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-GL-7966        TCGA-J7-6720 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
                   vv
clus                M0 M1 MX
  XQ GAIN CNV        1  0  2
  XQ GAIN WILD-TYPE 53  5 34
D29V7, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  M0           1                53
  M1           0                 5
  MX           2                34
                   vv
clus                 I II III IV
  XQ GAIN CNV        1  0   1  1
  XQ GAIN WILD-TYPE 52  7  23  8
D29V8, multiclass
     clus
vv    XQ GAIN CNV XQ GAIN WILD-TYPE
  I             1                52
  II            0                 7
  III           1                23
  IV            1                 8

Clustering(30) Variable = 1p loss
D30V1, survival
                   sevent
clus2                0  1
  1P LOSS CNV       10  1
  1P LOSS WILD-TYPE 73 13
      1P LOSS CNV 1P LOSS WILD-TYPE 
               11                86 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                13 
$`1P LOSS CNV`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5875 
        0.03         0.10         4.60         7.33         4.11        86.73 
TCGA-BQ-5882 TCGA-BQ-7044 TCGA-BQ-7055 TCGA-G7-6797 TCGA-G7-7502 
       21.63       123.58        26.27        12.72        14.07 

$`1P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        1.61         9.63        58.45        53.79        13.55        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       25.08        44.61        11.05         3.58         5.88         4.44 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
        4.83        50.50         0.69        10.82         3.02         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 TCGA-BQ-5877 
        1.08         0.62         6.44         1.18        19.23         8.84 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-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-7056 
       93.34        44.84        61.28        50.37        49.84        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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 
       32.12        41.33        11.05        30.51        34.82        14.63 
TCGA-GL-6846 TCGA-GL-7966 
      182.73         3.68 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.03              0.03 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           123.58            182.73 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           12.720            14.185 
[1] "0.0 - 123.6 (12.7)" "0.0 - 182.7 (14.2)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          3    8
  1P LOSS WILD-TYPE   31   62
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           3                31
  MALE             8                62
D30V4, continuous
                   vv
clus                T1 T2 T3+T4
  1P LOSS CNV        6  1     4
  1P LOSS WILD-TYPE 52 12    29
D30V5, multiclass
       clus
vv      1P LOSS CNV 1P LOSS WILD-TYPE
  T1              6                52
  T2              1                12
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  1P LOSS CNV        2  0  0
  1P LOSS WILD-TYPE 18 12  4
D30V6, multiclass
[1] "Remove cluster labels:" "1P LOSS CNV"           
clus
      1P LOSS CNV 1P LOSS WILD-TYPE 
                2                34 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3466        TCGA-AL-3473 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268        TCGA-BQ-5877 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5885 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889        TCGA-BQ-5890 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893        TCGA-BQ-5894 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050        TCGA-BQ-7051 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131        TCGA-G7-6789 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-GL-6846 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-J7-6720 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  1P LOSS CNV        6  0  4
  1P LOSS WILD-TYPE 48  5 32
D30V7, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  M0           6                48
  M1           0                 5
  MX           4                32
                   vv
clus                 I II III IV
  1P LOSS CNV        5  1   4  0
  1P LOSS WILD-TYPE 48  6  20  9
D30V8, multiclass
     clus
vv    1P LOSS CNV 1P LOSS WILD-TYPE
  I             5                48
  II            1                 6
  III           4                20
  IV            0                 9

Clustering(31) Variable = 1q loss
D31V1, survival
                   sevent
clus2                0  1
  1Q LOSS CNV        6  0
  1Q LOSS WILD-TYPE 77 14
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                6                91 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                0                14 
$`1Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 TCGA-B3-3926 TCGA-G7-6797 TCGA-G7-7502 
        0.03         0.10         7.33         4.11        12.72        14.07 

$`1Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 
       30.31        25.08        44.61        11.05         3.58         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        4.44         4.83        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         8.84        63.72        22.92        43.17        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.82         7.63         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 TCGA-G7-6790 
       54.87        15.48         5.85         5.26         6.84        32.12 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-6846 
       41.33        11.05        30.51        34.82        14.63       182.73 
TCGA-GL-7966 
        3.68 

      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             0.03              0.03 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
            14.07            182.73 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             5.72             14.63 
[1] "0.0 - 14.1 (5.7)"   "0.0 - 182.7 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"1Q LOSS WILD-TYPE" 
[1] "hr="     "9400000"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    4
  1Q LOSS WILD-TYPE   32   66
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  FEMALE           2                32
  MALE             4                66
D31V4, continuous
                   vv
clus                T1 T2 T3+T4
  1Q LOSS CNV        4  1     1
  1Q LOSS WILD-TYPE 54 12    32
D31V5, multiclass
       clus
vv      1Q LOSS CNV 1Q LOSS WILD-TYPE
  T1              4                54
  T2              1                12
  T3+T4           1                32
                   vv
clus                N0 N1 N2
  1Q LOSS CNV        1  0  0
  1Q LOSS WILD-TYPE 19 12  4
D31V6, multiclass
[1] "Remove cluster labels:" "1Q LOSS CNV"           
clus
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                1                35 
       TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3466        TCGA-AL-3473 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268        TCGA-BQ-5877 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5882 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-GL-7966        TCGA-J7-6720 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  1Q LOSS CNV        2  0  3
  1Q LOSS WILD-TYPE 52  5 33
D31V7, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  M0           2                52
  M1           0                 5
  MX           3                33
                   vv
clus                 I II III IV
  1Q LOSS CNV        3  1   1  0
  1Q LOSS WILD-TYPE 50  6  23  9
D31V8, multiclass
     clus
vv    1Q LOSS CNV 1Q LOSS WILD-TYPE
  I             3                50
  II            1                 6
  III           1                23
  IV            0                 9

Clustering(32) Variable = 3p loss
D32V1, survival
                   sevent
clus2                0  1
  3P LOSS CNV        4  2
  3P LOSS WILD-TYPE 79 12
      3P LOSS CNV 3P LOSS WILD-TYPE 
                6                91 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                12 
$`3P LOSS CNV`
TCGA-AL-3473 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 TCGA-GL-7966 
       25.08         8.84        21.63        11.97        79.82         3.68 

$`3P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       53.79        13.55        30.31        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
        6.44         1.18        86.73        19.23        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        47.80        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-5893 
       25.35        13.25        10.82         7.63         0.95         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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       14.63         3.02        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-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        30.51        34.82        12.72        14.63        14.07 
TCGA-GL-6846 
      182.73 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             3.68              0.03 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            79.82            182.73 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            16.80             13.74 
[1] "3.7 - 79.8 (16.8)"  "0.0 - 182.7 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3P LOSS CNV" 
[1] "hr=" "2.5"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          1    5
  3P LOSS WILD-TYPE   33   65
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           1                33
  MALE             5                65
D32V4, continuous
                   vv
clus                T1 T2 T3+T4
  3P LOSS CNV        1  1     4
  3P LOSS WILD-TYPE 57 12    29
D32V5, multiclass
       clus
vv      3P LOSS CNV 3P LOSS WILD-TYPE
  T1              1                57
  T2              1                12
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  3P LOSS CNV        3  3  0
  3P LOSS WILD-TYPE 17  9  4
D32V6, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  N0           3                17
  N1           3                 9
  N2           0                 4
                   vv
clus                M0 M1 MX
  3P LOSS CNV        3  1  2
  3P LOSS WILD-TYPE 51  4 34
D32V7, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  M0           3                51
  M1           1                 4
  MX           2                34
                   vv
clus                 I II III IV
  3P LOSS CNV        1  1   3  1
  3P LOSS WILD-TYPE 52  6  21  8
D32V8, multiclass
     clus
vv    3P LOSS CNV 3P LOSS WILD-TYPE
  I             1                52
  II            1                 6
  III           3                21
  IV            1                 8

Clustering(33) Variable = 3q loss
D33V1, survival
                   sevent
clus2                0  1
  3Q LOSS CNV        1  2
  3Q LOSS WILD-TYPE 82 12
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                94 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                12 
$`3Q LOSS CNV`
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-GL-7966 
        8.84        21.63         3.68 

$`3Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        7.33         3.58         4.11         5.88         4.44         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50         0.69        10.82         3.02         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
        0.62         6.44         1.18        86.73        19.23        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.17        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        6.84        32.12        41.33        11.05        30.51        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       12.72        14.63        14.07       182.73 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             3.68              0.03 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            21.63            182.73 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            8.840            13.905 
[1] "3.7 - 21.6 (8.8)"   "0.0 - 182.7 (13.9)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "3Q LOSS CNV" 
[1] "hr=" "18" 
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          1    2
  3Q LOSS WILD-TYPE   33   68
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           1                33
  MALE             2                68
D33V4, continuous
                   vv
clus                T1 T2 T3+T4
  3Q LOSS CNV        0  0     3
  3Q LOSS WILD-TYPE 58 13    30
D33V5, multiclass
       clus
vv      3Q LOSS CNV 3Q LOSS WILD-TYPE
  T1              0                58
  T2              0                13
  T3+T4           3                30
                   vv
clus                N0 N1 N2
  3Q LOSS CNV        1  2  0
  3Q LOSS WILD-TYPE 19 10  4
D33V6, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  N0           1                19
  N1           2                10
  N2           0                 4
                   vv
clus                M0 M1 MX
  3Q LOSS CNV        1  1  1
  3Q LOSS WILD-TYPE 53  4 35
D33V7, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  M0           1                53
  M1           1                 4
  MX           1                35
                   vv
clus                 I II III IV
  3Q LOSS CNV        0  0   2  1
  3Q LOSS WILD-TYPE 53  7  22  8
D33V8, multiclass
     clus
vv    3Q LOSS CNV 3Q LOSS WILD-TYPE
  I             0                53
  II            0                 7
  III           2                22
  IV            1                 8

Clustering(34) Variable = 4p loss
D34V1, survival
                   sevent
clus2                0  1
  4P LOSS CNV        6  2
  4P LOSS WILD-TYPE 77 12
      4P LOSS CNV 4P LOSS WILD-TYPE 
                8                89 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                2                12 
$`4P LOSS CNV`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-DZ-6131 
        0.69         7.33         4.11        22.92        21.63        79.82 
TCGA-G7-7501 TCGA-GL-7966 
       14.63         3.68 

$`4P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        11.05         3.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
        3.02         0.46         1.08         0.62         6.44         1.18 
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-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        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-G7-7502 TCGA-GL-6846 
       30.51        34.82        12.72        14.07       182.73 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             0.69              0.03 
      4P LOSS CNV 4P LOSS WILD-TYPE 
            79.82            182.73 
      4P LOSS CNV 4P LOSS WILD-TYPE 
            10.98             13.74 
[1] "0.7 - 79.8 (11.0)"  "0.0 - 182.7 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4P LOSS CNV" 
[1] "hr=" "2.6"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          6    2
  4P LOSS WILD-TYPE   28   68
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  FEMALE           6                28
  MALE             2                68
D34V4, continuous
[1] "Remove cluster labels:" "4P LOSS CNV"           
clus
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DW-7842        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-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G7-7502 
"4P LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  4P LOSS CNV        2  1     5
  4P LOSS WILD-TYPE 56 12    28
D34V5, multiclass
       clus
vv      4P LOSS CNV 4P LOSS WILD-TYPE
  T1              2                56
  T2              1                12
  T3+T4           5                28
                   vv
clus                N0 N1 N2
  4P LOSS CNV        2  3  0
  4P LOSS WILD-TYPE 18  9  4
D34V6, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  N0           2                18
  N1           3                 9
  N2           0                 4
                   vv
clus                M0 M1 MX
  4P LOSS CNV        3  0  5
  4P LOSS WILD-TYPE 51  5 31
D34V7, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  M0           3                51
  M1           0                 5
  MX           5                31
                   vv
clus                 I II III IV
  4P LOSS CNV        2  1   5  0
  4P LOSS WILD-TYPE 51  6  19  9
D34V8, multiclass
     clus
vv    4P LOSS CNV 4P LOSS WILD-TYPE
  I             2                51
  II            1                 6
  III           5                19
  IV            0                 9

Clustering(35) Variable = 4q loss
D35V1, survival
                   sevent
clus2                0  1
  4Q LOSS CNV        7  1
  4Q LOSS WILD-TYPE 76 13
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                8                89 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                1                13 
$`4Q LOSS CNV`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 
        0.69         7.33         4.11        19.23        21.63        79.82 
TCGA-G7-7501 TCGA-GL-7966 
       14.63         3.68 

$`4Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        11.05         3.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
        3.02         0.46         1.08         0.62         6.44         1.18 
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-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.74         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        3.02        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-G7-7502 TCGA-GL-6846 
       30.51        34.82        12.72        14.07       182.73 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             0.69              0.03 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            79.82            182.73 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            10.98             13.74 
[1] "0.7 - 79.8 (11.0)"  "0.0 - 182.7 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "4Q LOSS CNV" 
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          6    3
  4Q LOSS WILD-TYPE   28   67
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  FEMALE           6                28
  MALE             3                67
D35V4, continuous
[1] "Remove cluster labels:" "4Q LOSS CNV"           
clus
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DW-7842        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-G7-6790        TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G7-7502 
"4Q LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  4Q LOSS CNV        3  1     5
  4Q LOSS WILD-TYPE 55 12    28
D35V5, multiclass
       clus
vv      4Q LOSS CNV 4Q LOSS WILD-TYPE
  T1              3                55
  T2              1                12
  T3+T4           5                28
                   vv
clus                N0 N1 N2
  4Q LOSS CNV        2  2  0
  4Q LOSS WILD-TYPE 18 10  4
D35V6, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  N0           2                18
  N1           2                10
  N2           0                 4
                   vv
clus                M0 M1 MX
  4Q LOSS CNV        4  0  5
  4Q LOSS WILD-TYPE 50  5 31
D35V7, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  M0           4                50
  M1           0                 5
  MX           5                31
                   vv
clus                 I II III IV
  4Q LOSS CNV        3  1   5  0
  4Q LOSS WILD-TYPE 50  6  19  9
D35V8, multiclass
     clus
vv    4Q LOSS CNV 4Q LOSS WILD-TYPE
  I             3                50
  II            1                 6
  III           5                19
  IV            0                 9

Clustering(36) Variable = 5p loss
D36V1, survival
                   sevent
clus2                0  1
  5P LOSS CNV        2  2
  5P LOSS WILD-TYPE 81 12
      5P LOSS CNV 5P LOSS WILD-TYPE 
                4                93 
      5P LOSS CNV 5P LOSS WILD-TYPE 
                2                12 
$`5P LOSS CNV`
TCGA-A4-7286 TCGA-BQ-5879 TCGA-G7-6793 TCGA-GL-7966 
        0.03        22.92        11.05         3.68 

$`5P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        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-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       14.63        14.07       182.73 

      5P LOSS CNV 5P LOSS WILD-TYPE 
             0.03              0.03 
      5P LOSS CNV 5P LOSS WILD-TYPE 
            22.92            182.73 
      5P LOSS CNV 5P LOSS WILD-TYPE 
            7.365            14.070 
[1] "0.0 - 22.9 (7.4)"   "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5P LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        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-G7-6789        TCGA-G7-6790 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5P LOSS WILD-TYPE"       "5P LOSS CNV" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5P LOSS CNV" 
[1] "hr=" "11" 
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS CNV          3    1
  5P LOSS WILD-TYPE   31   69
        clus
vv       5P LOSS CNV 5P LOSS WILD-TYPE
  FEMALE           3                31
  MALE             1                69
D36V4, continuous
[1] "Remove cluster labels:" "5P LOSS CNV"           
clus
      5P LOSS CNV 5P LOSS WILD-TYPE 
                2                20 
       TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  5P LOSS CNV        0  0     4
  5P LOSS WILD-TYPE 58 13    29
D36V5, multiclass
       clus
vv      5P LOSS CNV 5P LOSS WILD-TYPE
  T1              0                58
  T2              0                13
  T3+T4           4                29
                   vv
clus                N0 N1 N2
  5P LOSS CNV        0  2  1
  5P LOSS WILD-TYPE 20 10  3
D36V6, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  N0           0                20
  N1           2                10
  N2           1                 3
                   vv
clus                M0 M1 MX
  5P LOSS CNV        1  0  2
  5P LOSS WILD-TYPE 53  5 34
D36V7, multiclass
    clus
vv   5P LOSS CNV 5P LOSS WILD-TYPE
  M0           1                53
  M1           0                 5
  MX           2                34
                   vv
clus                 I II III IV
  5P LOSS CNV        0  0   2  1
  5P LOSS WILD-TYPE 53  7  22  8
D36V8, multiclass
     clus
vv    5P LOSS CNV 5P LOSS WILD-TYPE
  I             0                53
  II            0                 7
  III           2                22
  IV            1                 8

Clustering(37) Variable = 5q loss
D37V1, survival
                   sevent
clus2                0  1
  5Q LOSS CNV        3  1
  5Q LOSS WILD-TYPE 80 13
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4                93 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                1                13 
$`5Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5879 TCGA-GL-7966 
        0.03         0.69        22.92         3.68 

$`5Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
        1.18        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-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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       14.63        14.07       182.73 

      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             0.03              0.03 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            22.92            182.73 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            2.185            14.070 
[1] "0.0 - 22.9 (2.2)"   "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5Q LOSS CNV" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "5Q LOSS CNV"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
      "5Q LOSS CNV" 
[1] "hr=" "7.5"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          3    1
  5Q LOSS WILD-TYPE   31   69
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  FEMALE           3                31
  MALE             1                69
D37V4, continuous
[1] "Remove cluster labels:" "5Q LOSS CNV"           
clus
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560        TCGA-DW-5561 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-7502 
"5Q LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  5Q LOSS CNV        1  0     3
  5Q LOSS WILD-TYPE 57 13    30
D37V5, multiclass
       clus
vv      5Q LOSS CNV 5Q LOSS WILD-TYPE
  T1              1                57
  T2              0                13
  T3+T4           3                30
                   vv
clus                N0 N1 N2
  5Q LOSS CNV        0  2  0
  5Q LOSS WILD-TYPE 20 10  4
D37V6, multiclass
[1] "Remove cluster labels:" "5Q LOSS CNV"           
clus
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                2                34 
       TCGA-A4-7583        TCGA-A4-7585        TCGA-A4-7915        TCGA-AL-3466 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398        TCGA-B9-7268 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5877        TCGA-BQ-5878        TCGA-BQ-5880        TCGA-BQ-5882 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5885        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7045        TCGA-BQ-7048        TCGA-BQ-7050 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BQ-7051        TCGA-BQ-7056        TCGA-BQ-7058        TCGA-DZ-6131 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G7-6789        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-GL-6846        TCGA-J7-6720 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
                   vv
clus                M0 M1 MX
  5Q LOSS CNV        1  0  2
  5Q LOSS WILD-TYPE 53  5 34
D37V7, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  M0           1                53
  M1           0                 5
  MX           2                34
                   vv
clus                 I II III IV
  5Q LOSS CNV        1  0   2  0
  5Q LOSS WILD-TYPE 52  7  22  9
D37V8, multiclass
     clus
vv    5Q LOSS CNV 5Q LOSS WILD-TYPE
  I             1                52
  II            0                 7
  III           2                22
  IV            0                 9

Clustering(38) Variable = 6p loss
D38V1, survival
                   sevent
clus2                0  1
  6P LOSS CNV        6  2
  6P LOSS WILD-TYPE 77 12
      6P LOSS CNV 6P LOSS WILD-TYPE 
                8                89 
      6P LOSS CNV 6P LOSS WILD-TYPE 
                2                12 
$`6P LOSS CNV`
TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5882 TCGA-BQ-7056 TCGA-EV-5902 TCGA-G7-6793 
        0.03         4.11        21.63        20.12         5.85        11.05 
TCGA-G7-6797 TCGA-G7-7502 
       12.72        14.07 

$`6P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        3.58         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        47.80        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-7058 
       44.84        61.28        50.37        49.84        26.27        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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.74         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        79.82        80.84        51.16        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-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-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       30.51        34.82        14.63       182.73         3.68 

      6P LOSS CNV 6P LOSS WILD-TYPE 
             0.03              0.03 
      6P LOSS CNV 6P LOSS WILD-TYPE 
            21.63            182.73 
      6P LOSS CNV 6P LOSS WILD-TYPE 
           11.885            14.630 
[1] "0.0 - 21.6 (11.9)"  "0.0 - 182.7 (14.6)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" "6P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
      "6P LOSS CNV" "6P LOSS WILD-TYPE"       "6P LOSS CNV" "6P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6P LOSS WILD-TYPE" 
[1] "hr=" "5.2"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS CNV          4    5
  6P LOSS WILD-TYPE   30   65
        clus
vv       6P LOSS CNV 6P LOSS WILD-TYPE
  FEMALE           4                30
  MALE             5                65
D38V4, continuous
                   vv
clus                T1 T2 T3+T4
  6P LOSS CNV        4  0     5
  6P LOSS WILD-TYPE 54 13    28
D38V5, multiclass
       clus
vv      6P LOSS CNV 6P LOSS WILD-TYPE
  T1              4                54
  T2              0                13
  T3+T4           5                28
                   vv
clus                N0 N1 N2
  6P LOSS CNV        2  0  1
  6P LOSS WILD-TYPE 18 12  3
D38V6, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  N0           2                18
  N1           0                12
  N2           1                 3
                   vv
clus                M0 M1 MX
  6P LOSS CNV        5  0  3
  6P LOSS WILD-TYPE 49  5 33
D38V7, multiclass
    clus
vv   6P LOSS CNV 6P LOSS WILD-TYPE
  M0           5                49
  M1           0                 5
  MX           3                33
                   vv
clus                 I II III IV
  6P LOSS CNV        3  0   4  1
  6P LOSS WILD-TYPE 50  7  20  8
D38V8, multiclass
     clus
vv    6P LOSS CNV 6P LOSS WILD-TYPE
  I             3                50
  II            0                 7
  III           4                20
  IV            1                 8

Clustering(39) Variable = 6q loss
D39V1, survival
                   sevent
clus2                0  1
  6Q LOSS CNV        7  2
  6Q LOSS WILD-TYPE 76 12
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                9                88 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                12 
$`6Q LOSS CNV`
TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-7056 
        0.03         4.11        86.73        21.63        13.25        20.12 
TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-7502 
        5.85        11.05        14.07 

$`6Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        3.58         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        1.18        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-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-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.37        49.84        26.27        11.28         7.63         7.00 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-5903 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        5.26         6.84        32.12        41.33        30.51        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       12.72        14.63       182.73         3.68 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             0.03              0.03 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            86.73            182.73 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
           13.250            14.185 
[1] "0.0 - 86.7 (13.2)"  "0.0 - 182.7 (14.2)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"6Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          6    4
  6Q LOSS WILD-TYPE   28   66
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  FEMALE           6                28
  MALE             4                66
D39V4, continuous
                   vv
clus                T1 T2 T3+T4
  6Q LOSS CNV        4  0     6
  6Q LOSS WILD-TYPE 54 13    27
D39V5, multiclass
       clus
vv      6Q LOSS CNV 6Q LOSS WILD-TYPE
  T1              4                54
  T2              0                13
  T3+T4           6                27
                   vv
clus                N0 N1 N2
  6Q LOSS CNV        3  0  1
  6Q LOSS WILD-TYPE 17 12  3
D39V6, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  N0           3                17
  N1           0                12
  N2           1                 3
                   vv
clus                M0 M1 MX
  6Q LOSS CNV        7  0  2
  6Q LOSS WILD-TYPE 47  5 34
D39V7, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           7                47
  M1           0                 5
  MX           2                34
                   vv
clus                 I II III IV
  6Q LOSS CNV        4  0   4  1
  6Q LOSS WILD-TYPE 49  7  20  8
D39V8, multiclass
     clus
vv    6Q LOSS CNV 6Q LOSS WILD-TYPE
  I             4                49
  II            0                 7
  III           4                20
  IV            1                 8

Clustering(40) Variable = 8p loss
D40V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV        3  0
  8P LOSS WILD-TYPE 80 14
      8P LOSS CNV 8P LOSS WILD-TYPE 
                3                94 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                0                14 
$`8P LOSS CNV`
TCGA-B1-7332 TCGA-B3-3926 TCGA-DW-5560 
        7.33         4.11        11.61 

$`8P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        3.58         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             4.11              0.03 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            11.61            182.73 
      8P LOSS CNV 8P LOSS WILD-TYPE 
             7.33             14.35 
[1] "4.1 - 11.6 (7.3)"   "0.0 - 182.7 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"8P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"8P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"8P LOSS WILD-TYPE" 
[1] "hr="     "9100000"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          3    0
  8P LOSS WILD-TYPE   31   70
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE           3                31
  MALE             0                70
D40V4, continuous
[1] "Remove cluster labels:" "8P LOSS CNV"           
clus
      8P LOSS CNV 8P LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5561 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G7-7502 
"8P LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  8P LOSS CNV        2  1     0
  8P LOSS WILD-TYPE 56 12    33
D40V5, multiclass
       clus
vv      8P LOSS CNV 8P LOSS WILD-TYPE
  T1              2                56
  T2              1                12
  T3+T4           0                33
                   vv
clus                N0 N1 N2
  8P LOSS CNV        0  0  0
  8P LOSS WILD-TYPE 20 12  4
D40V6, multiclass
                   vv
clus                M0 M1 MX
  8P LOSS CNV        2  0  1
  8P LOSS WILD-TYPE 52  5 35
D40V7, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  M0           2                52
  M1           0                 5
  MX           1                35
                   vv
clus                 I II III IV
  8P LOSS CNV        2  1   0  0
  8P LOSS WILD-TYPE 51  6  24  9
D40V8, multiclass
     clus
vv    8P LOSS CNV 8P LOSS WILD-TYPE
  I             2                51
  II            1                 6
  III           0                24
  IV            0                 9

Clustering(41) Variable = 9p loss
D41V1, survival
                   sevent
clus2                0  1
  9P LOSS CNV        9  3
  9P LOSS WILD-TYPE 74 11
      9P LOSS CNV 9P LOSS WILD-TYPE 
               12                85 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                3                11 
$`9P LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5879 
        0.03         0.69         9.63         4.11         3.02        22.92 
TCGA-BQ-5888 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       13.25        20.12        79.82        11.05        34.82        14.63 

$`9P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        1.61         4.60        58.45        53.79        13.55        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 
       25.08        44.61        11.05         7.33         3.58         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
        4.44         4.83        50.50         0.69        10.82         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 
        1.08         0.62         6.44         1.18        86.73        19.23 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6133 
       13.74         3.75        14.63         3.02        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-G7-6797 TCGA-G7-7502 TCGA-GL-6846 
       32.12        41.33        30.51        12.72        14.07       182.73 
TCGA-GL-7966 
        3.68 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             0.03              0.03 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            79.82            182.73 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            12.15             14.07 
[1] "0.0 - 79.8 (12.2)"  "0.0 - 182.7 (14.1)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9P LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9P LOSS WILD-TYPE" 
[1] "hr=" "3"  
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          9    4
  9P LOSS WILD-TYPE   25   66
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  FEMALE           9                25
  MALE             4                66
D41V4, continuous
                   vv
clus                T1 T2 T3+T4
  9P LOSS CNV        4  1     8
  9P LOSS WILD-TYPE 54 12    25
D41V5, multiclass
       clus
vv      9P LOSS CNV 9P LOSS WILD-TYPE
  T1              4                54
  T2              1                12
  T3+T4           8                25
                   vv
clus                N0 N1 N2
  9P LOSS CNV        3  3  1
  9P LOSS WILD-TYPE 17  9  3
D41V6, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  N0           3                17
  N1           3                 9
  N2           1                 3
                   vv
clus                M0 M1 MX
  9P LOSS CNV        5  1  5
  9P LOSS WILD-TYPE 49  4 31
D41V7, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  M0           5                49
  M1           1                 4
  MX           5                31
                   vv
clus                 I II III IV
  9P LOSS CNV        4  0   5  2
  9P LOSS WILD-TYPE 49  7  19  7
D41V8, multiclass
     clus
vv    9P LOSS CNV 9P LOSS WILD-TYPE
  I             4                49
  II            0                 7
  III           5                19
  IV            2                 7

Clustering(42) Variable = 9q loss
D42V1, survival
                   sevent
clus2                0  1
  9Q LOSS CNV        9  3
  9Q LOSS WILD-TYPE 74 11
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               12                85 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                3                11 
$`9Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5888 
        0.03         0.69         9.63         4.11        22.92        13.25 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       26.27        20.12        79.82        11.05        34.82        14.63 

$`9Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        1.61         4.60        58.45        53.79        13.55        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 
       25.08        44.61        11.05         7.33         3.58         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        4.44         4.83        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.23         8.84        63.72        43.17        47.80        21.63 
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-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       49.84        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 TCGA-DZ-6133 
       13.74         3.75        14.63         3.02        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-G7-6797 TCGA-G7-7502 TCGA-GL-6846 
       32.12        41.33        30.51        12.72        14.07       182.73 
TCGA-GL-7966 
        3.68 

      9Q LOSS CNV 9Q LOSS WILD-TYPE 
             0.03              0.03 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            79.82            182.73 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            13.94             13.74 
[1] "0.0 - 79.8 (13.9)"  "0.0 - 182.7 (13.7)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9Q LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
      "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        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-B3-8121 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-GL-7966 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "2.7"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          8    5
  9Q LOSS WILD-TYPE   26   65
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  FEMALE           8                26
  MALE             5                65
D42V4, continuous
                   vv
clus                T1 T2 T3+T4
  9Q LOSS CNV        5  0     8
  9Q LOSS WILD-TYPE 53 13    25
D42V5, multiclass
       clus
vv      9Q LOSS CNV 9Q LOSS WILD-TYPE
  T1              5                53
  T2              0                13
  T3+T4           8                25
                   vv
clus                N0 N1 N2
  9Q LOSS CNV        3  3  1
  9Q LOSS WILD-TYPE 17  9  3
D42V6, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  N0           3                17
  N1           3                 9
  N2           1                 3
                   vv
clus                M0 M1 MX
  9Q LOSS CNV        6  1  5
  9Q LOSS WILD-TYPE 48  4 31
D42V7, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  M0           6                48
  M1           1                 4
  MX           5                31
                   vv
clus                 I II III IV
  9Q LOSS CNV        5  0   5  2
  9Q LOSS WILD-TYPE 48  7  19  7
D42V8, multiclass
     clus
vv    9Q LOSS CNV 9Q LOSS WILD-TYPE
  I             5                48
  II            0                 7
  III           5                19
  IV            2                 7

Clustering(43) Variable = 10p loss
D43V1, survival
                    sevent
clus2                 0  1
  10P LOSS CNV        5  1
  10P LOSS WILD-TYPE 78 13
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 6                 91 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 1                 13 
$`10P LOSS CNV`
TCGA-AL-3466 TCGA-B9-4116 TCGA-BQ-5876 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
        9.63         3.02        19.23        14.63        14.07         3.68 

$`10P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        1.18        86.73         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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-GL-6846 
      182.73 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              3.02               0.03 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             19.23             182.73 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             11.85              13.74 
[1] "3.0 - 19.2 (11.9)"  "0.0 - 182.7 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10P LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10P LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10P LOSS CNV" 
[1] "hr=" "3.2"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          3    3
  10P LOSS WILD-TYPE   31   67
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            3                 31
  MALE              3                 67
D43V4, continuous
                    vv
clus                 T1 T2 T3+T4
  10P LOSS CNV        2  1     3
  10P LOSS WILD-TYPE 56 12    30
D43V5, multiclass
       clus
vv      10P LOSS CNV 10P LOSS WILD-TYPE
  T1               2                 56
  T2               1                 12
  T3+T4            3                 30
                    vv
clus                 N0 N1 N2
  10P LOSS CNV        0  3  0
  10P LOSS WILD-TYPE 20  9  4
D43V6, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  N0            0                 20
  N1            3                  9
  N2            0                  4
                    vv
clus                 M0 M1 MX
  10P LOSS CNV        1  1  3
  10P LOSS WILD-TYPE 53  4 33
D43V7, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  M0            1                 53
  M1            1                  4
  MX            3                 33
                    vv
clus                  I II III IV
  10P LOSS CNV        2  0   2  1
  10P LOSS WILD-TYPE 51  7  22  8
D43V8, multiclass
     clus
vv    10P LOSS CNV 10P LOSS WILD-TYPE
  I              2                 51
  II             0                  7
  III            2                 22
  IV             1                  8

Clustering(44) Variable = 10q loss
D44V1, survival
                    sevent
clus2                 0  1
  10Q LOSS CNV        4  2
  10Q LOSS WILD-TYPE 79 12
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 6                 91 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                 12 
$`10Q LOSS CNV`
TCGA-AL-3466 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-7966 
        9.63        19.23        21.63        14.63        14.07         3.68 

$`10Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 
        0.89         0.23         1.61         4.60        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        6.44         1.18        86.73         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        47.80        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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-GL-6846 
      182.73 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              3.68               0.03 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             21.63             182.73 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             14.35              13.61 
[1] "3.7 - 21.6 (14.4)"  "0.0 - 182.7 (13.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "10Q LOSS CNV" 
[1] "hr=" "5.6"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          2    4
  10Q LOSS WILD-TYPE   32   66
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            2                 32
  MALE              4                 66
D44V4, continuous
                    vv
clus                 T1 T2 T3+T4
  10Q LOSS CNV        2  0     4
  10Q LOSS WILD-TYPE 56 13    29
D44V5, multiclass
       clus
vv      10Q LOSS CNV 10Q LOSS WILD-TYPE
  T1               2                 56
  T2               0                 13
  T3+T4            4                 29
                    vv
clus                 N0 N1 N2
  10Q LOSS CNV        1  3  0
  10Q LOSS WILD-TYPE 19  9  4
D44V6, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  N0            1                 19
  N1            3                  9
  N2            0                  4
                    vv
clus                 M0 M1 MX
  10Q LOSS CNV        2  1  3
  10Q LOSS WILD-TYPE 52  4 33
D44V7, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  M0            2                 52
  M1            1                  4
  MX            3                 33
                    vv
clus                  I II III IV
  10Q LOSS CNV        2  0   3  1
  10Q LOSS WILD-TYPE 51  7  21  8
D44V8, multiclass
     clus
vv    10Q LOSS CNV 10Q LOSS WILD-TYPE
  I              2                 51
  II             0                  7
  III            3                 21
  IV             1                  8

Clustering(45) Variable = 11p loss
D45V1, survival
                    sevent
clus2                 0  1
  11P LOSS CNV        5  2
  11P LOSS WILD-TYPE 78 12
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 7                 90 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                 12 
$`11P LOSS CNV`
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 
        0.69         7.33         4.44        19.23         8.84        21.63 
TCGA-G7-7502 
       14.07 

$`11P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        4.11         5.88         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
        3.02         0.46         1.08         0.62         6.44         1.18 
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-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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       30.51        34.82        12.72        14.63       182.73         3.68 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.69               0.03 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             21.63             182.73 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             8.840             14.185 
[1] "0.7 - 21.6 (8.8)"   "0.0 - 182.7 (14.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11P LOSS WILD-TYPE"       "11P LOSS CNV"       "11P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11P LOSS WILD-TYPE"       "11P LOSS CNV"       "11P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11P LOSS WILD-TYPE"       "11P LOSS CNV"       "11P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11P LOSS WILD-TYPE" 
[1] "hr=" "7.6"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          3    5
  11P LOSS WILD-TYPE   31   65
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  FEMALE            3                 31
  MALE              5                 65
D45V4, continuous
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6793 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  11P LOSS CNV        3  2     3
  11P LOSS WILD-TYPE 55 11    30
D45V5, multiclass
       clus
vv      11P LOSS CNV 11P LOSS WILD-TYPE
  T1               3                 55
  T2               2                 11
  T3+T4            3                 30
                    vv
clus                 N0 N1 N2
  11P LOSS CNV        1  1  0
  11P LOSS WILD-TYPE 19 11  4
D45V6, multiclass
[1] "Remove cluster labels:" "11P LOSS CNV"          
clus
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 2                 34 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3473         TCGA-AL-7173 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B9-7268         TCGA-BQ-5878 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5885 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-DZ-6131 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6793         TCGA-G7-6795 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-GL-6846         TCGA-GL-7966 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-J7-6720 
"11P LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  11P LOSS CNV        4  1  3
  11P LOSS WILD-TYPE 50  4 33
D45V7, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  M0            4                 50
  M1            1                  4
  MX            3                 33
                    vv
clus                  I II III IV
  11P LOSS CNV        3  2   2  1
  11P LOSS WILD-TYPE 50  5  22  8
D45V8, multiclass
     clus
vv    11P LOSS CNV 11P LOSS WILD-TYPE
  I              3                 50
  II             2                  5
  III            2                 22
  IV             1                  8

Clustering(46) Variable = 11q loss
D46V1, survival
                    sevent
clus2                 0  1
  11Q LOSS CNV        5  3
  11Q LOSS WILD-TYPE 78 11
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 8                 89 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 3                 11 
$`11Q LOSS CNV`
TCGA-B1-7332 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5890 TCGA-BQ-7044 
        7.33        19.23         8.84        21.63         7.63       123.58 
TCGA-G7-6793 TCGA-G7-7502 
       11.05        14.07 

$`11Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        6.44         1.18        86.73        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-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.82         0.95        11.97         7.89         2.76 
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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       34.82        12.72        14.63       182.73         3.68 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              7.33               0.03 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
            123.58             182.73 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             12.56              13.74 
[1] "7.3 - 123.6 (12.6)" "0.0 - 182.7 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "4.1"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          3    6
  11Q LOSS WILD-TYPE   31   64
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  FEMALE            3                 31
  MALE              6                 64
D46V4, continuous
[1] "Remove cluster labels:" "11Q LOSS CNV"          
clus
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  11Q LOSS CNV        2  1     6
  11Q LOSS WILD-TYPE 56 12    27
D46V5, multiclass
       clus
vv      11Q LOSS CNV 11Q LOSS WILD-TYPE
  T1               2                 56
  T2               1                 12
  T3+T4            6                 27
                    vv
clus                 N0 N1 N2
  11Q LOSS CNV        2  1  1
  11Q LOSS WILD-TYPE 18 11  3
D46V6, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  N0            2                 18
  N1            1                 11
  N2            1                  3
                    vv
clus                 M0 M1 MX
  11Q LOSS CNV        5  1  3
  11Q LOSS WILD-TYPE 49  4 33
D46V7, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  M0            5                 49
  M1            1                  4
  MX            3                 33
                    vv
clus                  I II III IV
  11Q LOSS CNV        2  1   4  2
  11Q LOSS WILD-TYPE 51  6  20  7
D46V8, multiclass
     clus
vv    11Q LOSS CNV 11Q LOSS WILD-TYPE
  I              2                 51
  II             1                  6
  III            4                 20
  IV             2                  7

Clustering(47) Variable = 13q loss
D47V1, survival
                    sevent
clus2                 0  1
  13Q LOSS CNV        6  3
  13Q LOSS WILD-TYPE 77 11
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 88 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 3                 11 
$`13Q LOSS CNV`
TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5879 TCGA-BQ-5882 
        0.69         0.23         4.11        86.73        22.92        21.63 
TCGA-G7-6793 TCGA-G7-7502 TCGA-GL-7966 
       11.05        14.07         3.68 

$`13Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 
       30.31        25.08        44.61        11.05         7.33         3.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
        3.02         0.46         1.08         0.62         6.44         1.18 
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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-G7-7501 TCGA-GL-6846 
       34.82        12.72        14.63       182.73 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              0.23               0.03 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             86.73             182.73 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
            11.050             14.185 
[1] "0.2 - 86.7 (11.1)"  "0.0 - 182.7 (14.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "13Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "13Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "13Q LOSS CNV" 
[1] "hr=" "3.9"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          7    2
  13Q LOSS WILD-TYPE   27   68
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            7                 27
  MALE              2                 68
D47V4, continuous
[1] "Remove cluster labels:" "13Q LOSS CNV"          
clus
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  13Q LOSS CNV        3  1     5
  13Q LOSS WILD-TYPE 55 12    28
D47V5, multiclass
       clus
vv      13Q LOSS CNV 13Q LOSS WILD-TYPE
  T1               3                 55
  T2               1                 12
  T3+T4            5                 28
                    vv
clus                 N0 N1 N2
  13Q LOSS CNV        2  2  1
  13Q LOSS WILD-TYPE 18 10  3
D47V6, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  N0            2                 18
  N1            2                 10
  N2            1                  3
                    vv
clus                 M0 M1 MX
  13Q LOSS CNV        4  0  5
  13Q LOSS WILD-TYPE 50  5 31
D47V7, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0            4                 50
  M1            0                  5
  MX            5                 31
                    vv
clus                  I II III IV
  13Q LOSS CNV        3  1   4  1
  13Q LOSS WILD-TYPE 50  6  20  8
D47V8, multiclass
     clus
vv    13Q LOSS CNV 13Q LOSS WILD-TYPE
  I              3                 50
  II             1                  6
  III            4                 20
  IV             1                  8

Clustering(48) Variable = 14q loss
D48V1, survival
                    sevent
clus2                 0  1
  14Q LOSS CNV       17  2
  14Q LOSS WILD-TYPE 66 12
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                19                 78 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 2                 12 
$`14Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 
        0.03         0.69         0.10         4.60         9.63        25.08 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5885 
       44.61         7.33         4.11         3.02        19.23        30.28 
TCGA-BQ-5888 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       13.25        79.82        80.84        11.05        34.82        14.63 
TCGA-G7-7502 
       14.07 

$`14Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       15.95        35.18         0.03         0.89         0.23         1.61 
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-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-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-5889 TCGA-BQ-5890 
       40.83        26.04        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-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 
       24.46        13.74         3.75        14.63         3.02        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-G7-6797 TCGA-GL-6846 TCGA-GL-7966 
       32.12        41.33        30.51        12.72       182.73         3.68 

      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              0.03               0.03 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             80.84             182.73 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
            13.250             14.185 
[1] "0.0 - 80.8 (13.2)"  "0.0 - 182.7 (14.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"14Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"14Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "14Q LOSS CNV"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"14Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          8   11
  14Q LOSS WILD-TYPE   26   59
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  FEMALE            8                 26
  MALE             11                 59
D48V4, continuous
                    vv
clus                 T1 T2 T3+T4
  14Q LOSS CNV        9  3     7
  14Q LOSS WILD-TYPE 49 10    26
D48V5, multiclass
       clus
vv      14Q LOSS CNV 14Q LOSS WILD-TYPE
  T1               9                 49
  T2               3                 10
  T3+T4            7                 26
                    vv
clus                 N0 N1 N2
  14Q LOSS CNV        4  3  2
  14Q LOSS WILD-TYPE 16  9  2
D48V6, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  N0            4                 16
  N1            3                  9
  N2            2                  2
                    vv
clus                 M0 M1 MX
  14Q LOSS CNV        7  1  9
  14Q LOSS WILD-TYPE 47  4 27
D48V7, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  M0            7                 47
  M1            1                  4
  MX            9                 27
                    vv
clus                  I II III IV
  14Q LOSS CNV        9  2   3  3
  14Q LOSS WILD-TYPE 44  5  21  6
D48V8, multiclass
     clus
vv    14Q LOSS CNV 14Q LOSS WILD-TYPE
  I              9                 44
  II             2                  5
  III            3                 21
  IV             3                  6

Clustering(49) Variable = 15q loss
D49V1, survival
                    sevent
clus2                 0  1
  15Q LOSS CNV        7  2
  15Q LOSS WILD-TYPE 76 12
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 9                 88 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 2                 12 
$`15Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-5398 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 
        0.03         0.10        11.05         4.11        22.92        21.63 
TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-7966 
       34.82        14.07         3.68 

$`15Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69        15.95        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 
       30.31        25.08        44.61         7.33         3.58         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        4.44         4.83        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-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-DW-7834 TCGA-DW-7836 
        7.13         3.78        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.74         3.75        14.63         3.02 
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-G7-6797 TCGA-G7-7501 TCGA-GL-6846 
       30.51        12.72        14.63       182.73 

      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              0.03               0.03 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
             34.82             182.73 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
            11.050             14.185 
[1] "0.0 - 34.8 (11.1)"  "0.0 - 182.7 (14.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "15Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "15Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "15Q LOSS CNV" 
[1] "hr=" "4.1"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          4    6
  15Q LOSS WILD-TYPE   30   64
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  FEMALE            4                 30
  MALE              6                 64
D49V4, continuous
                    vv
clus                 T1 T2 T3+T4
  15Q LOSS CNV        4  0     6
  15Q LOSS WILD-TYPE 54 13    27
D49V5, multiclass
       clus
vv      15Q LOSS CNV 15Q LOSS WILD-TYPE
  T1               4                 54
  T2               0                 13
  T3+T4            6                 27
                    vv
clus                 N0 N1 N2
  15Q LOSS CNV        3  2  0
  15Q LOSS WILD-TYPE 17 10  4
D49V6, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  N0            3                 17
  N1            2                 10
  N2            0                  4
                    vv
clus                 M0 M1 MX
  15Q LOSS CNV        6  0  3
  15Q LOSS WILD-TYPE 48  5 33
D49V7, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  M0            6                 48
  M1            0                  5
  MX            3                 33
                    vv
clus                  I II III IV
  15Q LOSS CNV        4  0   5  0
  15Q LOSS WILD-TYPE 49  7  19  9
D49V8, multiclass
     clus
vv    15Q LOSS CNV 15Q LOSS WILD-TYPE
  I              4                 49
  II             0                  7
  III            5                 19
  IV             0                  9

Clustering(50) Variable = 16q loss
D50V1, survival
                    sevent
clus2                 0  1
  16Q LOSS CNV        1  1
  16Q LOSS WILD-TYPE 82 13
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 2                 95 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 13 
$`16Q LOSS CNV`
TCGA-A4-7287 TCGA-G7-6793 
        0.69        11.05 

$`16Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 
       13.55        30.31        25.08        44.61        11.05         7.33 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        3.58         4.11         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        0.69        10.82         3.02         0.46         1.08         0.62 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        6.44         1.18        86.73        19.23         8.84        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.17        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.82         7.63 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.00         7.13 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
       24.46        13.74         3.75        14.63         3.02        79.82 
TCGA-DZ-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-G7-6795 TCGA-G7-6796 
        5.26         6.84        32.12        41.33        30.51        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       12.72        14.63        14.07       182.73         3.68 

      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              0.69               0.03 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             11.05             182.73 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              5.87              14.07 
[1] "0.7 - 11.1 (5.9)"   "0.0 - 182.7 (14.1)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"16Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"16Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"16Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 2                 95 
        TCGA-A4-7286         TCGA-A4-7288         TCGA-A4-7583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7732         TCGA-A4-7734 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-8098 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3467         TCGA-AL-3468 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3471         TCGA-AL-3472         TCGA-AL-3473 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-7332 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3925         TCGA-B3-3926         TCGA-B3-4103 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-4104         TCGA-B3-8121         TCGA-B9-4113 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4114         TCGA-B9-4115         TCGA-B9-4116 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-4617         TCGA-B9-5155 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-5156         TCGA-B9-7268         TCGA-BQ-5875 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6795         TCGA-G7-6796 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D50V2, continuous
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 2                 99 
        TCGA-A4-7286         TCGA-A4-7288         TCGA-A4-7583 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-8098         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B1-7332         TCGA-B3-3925 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4114 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4116         TCGA-B9-4117 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-4617         TCGA-B9-5155         TCGA-B9-5156 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5875         TCGA-BQ-5876 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-J7-6720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          3    0
  16Q LOSS WILD-TYPE   31   70
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  FEMALE            3                 31
  MALE              0                 70
D50V4, continuous
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6796 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  16Q LOSS CNV        1  0     2
  16Q LOSS WILD-TYPE 57 13    31
D50V5, multiclass
       clus
vv      16Q LOSS CNV 16Q LOSS WILD-TYPE
  T1               1                 57
  T2               0                 13
  T3+T4            2                 31
                    vv
clus                 N0 N1 N2
  16Q LOSS CNV        0  0  1
  16Q LOSS WILD-TYPE 20 12  3
D50V6, multiclass
[1] "Remove cluster labels:" "16Q LOSS CNV"          
clus
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 1                 35 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3473         TCGA-AL-7173 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B9-7268         TCGA-BQ-5877 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7045         TCGA-BQ-7048 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7056 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-DZ-6131         TCGA-G7-6789 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-GL-6846 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-GL-7966         TCGA-J7-6720 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
                    vv
clus                 M0 M1 MX
  16Q LOSS CNV        1  0  2
  16Q LOSS WILD-TYPE 53  5 34
D50V7, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  M0            1                 53
  M1            0                  5
  MX            2                 34
                    vv
clus                  I II III IV
  16Q LOSS CNV        1  0   1  1
  16Q LOSS WILD-TYPE 52  7  23  8
D50V8, multiclass
     clus
vv    16Q LOSS CNV 16Q LOSS WILD-TYPE
  I              1                 52
  II             0                  7
  III            1                 23
  IV             1                  8

Clustering(51) Variable = 17p loss
D51V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV        2  2
  17P LOSS WILD-TYPE 81 12
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 4                 93 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 2                 12 
$`17P LOSS CNV`
TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-3466 TCGA-G7-6793 
        0.69         0.23         9.63        11.05 

$`17P LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        1.61         4.60        58.45        53.79        13.55        30.31 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-3926 
       25.08        44.61        11.05         7.33         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
        3.02         0.46         1.08         0.62         6.44         1.18 
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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       32.12        41.33        30.51        34.82        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.07       182.73         3.68 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              0.23               0.03 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             11.05             182.73 
      17P LOSS CNV 17P LOSS WILD-TYPE 
              5.16              14.63 
[1] "0.2 - 11.1 (5.2)"   "0.0 - 182.7 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"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-DW-7834         TCGA-DW-7836 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"17P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"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-DW-7834         TCGA-DW-7836 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"17P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B1-7332         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-B3-8121 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"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-DW-7834         TCGA-DW-7836 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"17P LOSS WILD-TYPE" 
[1] "hr=" "26" 
D51V2, continuous
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV          4    1
  17P LOSS WILD-TYPE   30   69
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  FEMALE            4                 30
  MALE              1                 69
D51V4, continuous
[1] "Remove cluster labels:" "17P LOSS CNV"          
clus
      17P LOSS CNV 17P LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-DW-5560 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"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-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  17P LOSS CNV        1  1     3
  17P LOSS WILD-TYPE 57 12    30
D51V5, multiclass
       clus
vv      17P LOSS CNV 17P LOSS WILD-TYPE
  T1               1                 57
  T2               1                 12
  T3+T4            3                 30
                    vv
clus                 N0 N1 N2
  17P LOSS CNV        1  1  1
  17P LOSS WILD-TYPE 19 11  3
D51V6, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  N0            1                 19
  N1            1                 11
  N2            1                  3
                    vv
clus                 M0 M1 MX
  17P LOSS CNV        1  1  3
  17P LOSS WILD-TYPE 53  4 33
D51V7, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  M0            1                 53
  M1            1                  4
  MX            3                 33
                    vv
clus                  I II III IV
  17P LOSS CNV        1  1   1  2
  17P LOSS WILD-TYPE 52  6  23  7
D51V8, multiclass
     clus
vv    17P LOSS CNV 17P LOSS WILD-TYPE
  I              1                 52
  II             1                  6
  III            1                 23
  IV             2                  7

Clustering(52) Variable = 18p loss
D52V1, survival
                    sevent
clus2                 0  1
  18P LOSS CNV       10  4
  18P LOSS WILD-TYPE 73 10
      18P LOSS CNV 18P LOSS WILD-TYPE 
                14                 83 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 10 
$`18P LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-B1-7332 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 
        0.03         0.69         7.33         3.02         8.84        22.92 
TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-7044 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7840 
       21.63        25.35       123.58        11.28         7.63         3.75 
TCGA-EV-5903 TCGA-GL-7966 
        5.26         3.68 

$`18P LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       19.23        63.72        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.89         2.76        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-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46        13.74        14.63         3.02 
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-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       34.82        12.72        14.63        14.07       182.73 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              0.03               0.03 
      18P LOSS CNV 18P LOSS WILD-TYPE 
            123.58             182.73 
      18P LOSS CNV 18P LOSS WILD-TYPE 
              7.48              14.63 
[1] "0.0 - 123.6 (7.5)"  "0.0 - 182.7 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18P LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18P LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18P LOSS CNV"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18P LOSS CNV" 
[1] "hr=" "5.2"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          5   10
  18P LOSS WILD-TYPE   29   60
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  FEMALE            5                 29
  MALE             10                 60
D52V4, continuous
                    vv
clus                 T1 T2 T3+T4
  18P LOSS CNV        5  2     8
  18P LOSS WILD-TYPE 53 11    25
D52V5, multiclass
       clus
vv      18P LOSS CNV 18P LOSS WILD-TYPE
  T1               5                 53
  T2               2                 11
  T3+T4            8                 25
                    vv
clus                 N0 N1 N2
  18P LOSS CNV        2  3  1
  18P LOSS WILD-TYPE 18  9  3
D52V6, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  N0            2                 18
  N1            3                  9
  N2            1                  3
                    vv
clus                 M0 M1 MX
  18P LOSS CNV        7  1  5
  18P LOSS WILD-TYPE 47  4 31
D52V7, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  M0            7                 47
  M1            1                  4
  MX            5                 31
                    vv
clus                  I II III IV
  18P LOSS CNV        5  1   6  1
  18P LOSS WILD-TYPE 48  6  18  8
D52V8, multiclass
     clus
vv    18P LOSS CNV 18P LOSS WILD-TYPE
  I              5                 48
  II             1                  6
  III            6                 18
  IV             1                  8

Clustering(53) Variable = 18q loss
D53V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV       10  4
  18Q LOSS WILD-TYPE 73 10
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                14                 83 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 4                 10 
$`18Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7287 TCGA-B1-7332 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 
        0.03         0.69         7.33         3.02         8.84        22.92 
TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-7044 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-DW-7840 
       21.63        25.35       123.58        11.28         7.63         3.75 
TCGA-EV-5903 TCGA-GL-7966 
        5.26         3.68 

$`18Q LOSS WILD-TYPE`
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       15.95         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        1.61         4.60         9.63        58.45        53.79        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-3926 
       30.31        25.08        44.61        11.05         3.58         4.11 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        5.88         4.44         4.83        50.50         0.69        10.82 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5875 
        0.46         1.08         0.62         6.44         1.18        86.73 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       19.23        63.72        43.17        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.89         2.76        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-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.00         7.13         3.78        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
       35.93        37.55        24.46        13.74        14.63         3.02 
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-G7-7501 TCGA-G7-7502 TCGA-GL-6846 
       34.82        12.72        14.63        14.07       182.73 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.03               0.03 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
            123.58             182.73 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              7.48              14.63 
[1] "0.0 - 123.6 (7.5)"  "0.0 - 182.7 (14.6)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
      "18Q LOSS CNV"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "18Q LOSS CNV" 
[1] "hr=" "5.2"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          6   10
  18Q LOSS WILD-TYPE   28   60
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE            6                 28
  MALE             10                 60
D53V4, continuous
                    vv
clus                 T1 T2 T3+T4
  18Q LOSS CNV        5  2     9
  18Q LOSS WILD-TYPE 53 11    24
D53V5, multiclass
       clus
vv      18Q LOSS CNV 18Q LOSS WILD-TYPE
  T1               5                 53
  T2               2                 11
  T3+T4            9                 24
                    vv
clus                 N0 N1 N2
  18Q LOSS CNV        2  3  1
  18Q LOSS WILD-TYPE 18  9  3
D53V6, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  N0            2                 18
  N1            3                  9
  N2            1                  3
                    vv
clus                 M0 M1 MX
  18Q LOSS CNV        8  1  5
  18Q LOSS WILD-TYPE 46  4 31
D53V7, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  M0            8                 46
  M1            1                  4
  MX            5                 31
                    vv
clus                  I II III IV
  18Q LOSS CNV        5  1   7  1
  18Q LOSS WILD-TYPE 48  6  17  8
D53V8, multiclass
     clus
vv    18Q LOSS CNV 18Q LOSS WILD-TYPE
  I              5                 48
  II             1                  6
  III            7                 17
  IV             1                  8

Clustering(54) Variable = 19p loss
D54V1, survival
                    sevent
clus2                 0  1
  19P LOSS CNV        4  0
  19P LOSS WILD-TYPE 79 14
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 4                 93 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 0                 14 
$`19P LOSS CNV`
TCGA-A4-7286 TCGA-B1-7332 TCGA-BQ-5876 TCGA-G7-7502 
        0.03         7.33        19.23        14.07 

$`19P LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
        1.18        86.73         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-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       14.63       182.73         3.68 

      19P LOSS CNV 19P LOSS WILD-TYPE 
              0.03               0.03 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             19.23             182.73 
      19P LOSS CNV 19P LOSS WILD-TYPE 
             10.70              13.74 
[1] "0.0 - 19.2 (10.7)"  "0.0 - 182.7 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19P LOSS WILD-TYPE"       "19P LOSS CNV" "19P LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19P LOSS WILD-TYPE" 
[1] "hr="     "9400000"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          1    3
  19P LOSS WILD-TYPE   33   67
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  FEMALE            1                 33
  MALE              3                 67
D54V4, continuous
[1] "Remove cluster labels:" "19P LOSS CNV"          
clus
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7828         TCGA-AL-3466         TCGA-DW-5560 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  19P LOSS CNV        2  1     1
  19P LOSS WILD-TYPE 56 12    32
D54V5, multiclass
       clus
vv      19P LOSS CNV 19P LOSS WILD-TYPE
  T1               2                 56
  T2               1                 12
  T3+T4            1                 32
                    vv
clus                 N0 N1 N2
  19P LOSS CNV        0  0  0
  19P LOSS WILD-TYPE 20 12  4
D54V6, multiclass
                    vv
clus                 M0 M1 MX
  19P LOSS CNV        1  0  2
  19P LOSS WILD-TYPE 53  5 34
D54V7, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  M0            1                 53
  M1            0                  5
  MX            2                 34
                    vv
clus                  I II III IV
  19P LOSS CNV        2  1   0  0
  19P LOSS WILD-TYPE 51  6  24  9
D54V8, multiclass
     clus
vv    19P LOSS CNV 19P LOSS WILD-TYPE
  I              2                 51
  II             1                  6
  III            0                 24
  IV             0                  9

Clustering(55) Variable = 19q loss
D55V1, survival
                    sevent
clus2                 0  1
  19Q LOSS CNV        3  0
  19Q LOSS WILD-TYPE 80 14
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                 94 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 0                 14 
$`19Q LOSS CNV`
TCGA-A4-7286 TCGA-B1-7332 TCGA-G7-7502 
        0.03         7.33        14.07 

$`19Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.69        15.95         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        0.23         1.61         4.60         9.63        58.45        53.79 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 
       13.55        30.31        25.08        44.61        11.05         3.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
        4.11         5.88         4.44         4.83        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-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.00         7.13         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.16        61.02        54.87        15.48         5.85         5.26 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        6.84        32.12        41.33        11.05        30.51        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-6846 TCGA-GL-7966 
       12.72        14.63       182.73         3.68 

      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              0.03               0.03 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             14.07             182.73 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             7.330             14.185 
[1] "0.0 - 14.1 (7.3)"   "0.0 - 182.7 (14.2)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
"19Q LOSS WILD-TYPE" 
[1] "hr="     "9100000"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          1    2
  19Q LOSS WILD-TYPE   33   68
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  FEMALE            1                 33
  MALE              2                 68
D55V4, continuous
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 20 
        TCGA-A4-7828         TCGA-AL-3466         TCGA-DW-5560 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  19Q LOSS CNV        1  1     1
  19Q LOSS WILD-TYPE 57 12    32
D55V5, multiclass
       clus
vv      19Q LOSS CNV 19Q LOSS WILD-TYPE
  T1               1                 57
  T2               1                 12
  T3+T4            1                 32
                    vv
clus                 N0 N1 N2
  19Q LOSS CNV        0  0  0
  19Q LOSS WILD-TYPE 20 12  4
D55V6, multiclass
                    vv
clus                 M0 M1 MX
  19Q LOSS CNV        0  0  2
  19Q LOSS WILD-TYPE 54  5 34
D55V7, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 93 
        TCGA-A4-7287         TCGA-A4-7288         TCGA-A4-7583 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7584         TCGA-A4-7585         TCGA-A4-7732 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7828         TCGA-A4-7915 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7996         TCGA-A4-8098         TCGA-AL-3466 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3467         TCGA-AL-3468         TCGA-AL-3471 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-3473         TCGA-AL-7173 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B1-5398         TCGA-B3-3925         TCGA-B3-3926 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5875         TCGA-BQ-5876 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5877         TCGA-BQ-5878         TCGA-BQ-5879 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5880         TCGA-BQ-5881         TCGA-BQ-5882 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5883         TCGA-BQ-5884         TCGA-BQ-5885 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5886         TCGA-BQ-5887         TCGA-BQ-5888 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7044         TCGA-BQ-7045         TCGA-BQ-7046 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7049         TCGA-BQ-7050 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7053         TCGA-BQ-7055 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-BQ-7058         TCGA-BQ-7059 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7060         TCGA-BQ-7061         TCGA-BQ-7062 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-DZ-6131         TCGA-DZ-6132 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6133         TCGA-DZ-6134         TCGA-DZ-6135 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-GL-6846 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-7966         TCGA-HE-7128 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7129         TCGA-HE-7130         TCGA-J7-6720 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
                    vv
clus                  I II III IV
  19Q LOSS CNV        1  1   0  0
  19Q LOSS WILD-TYPE 52  6  24  9
D55V8, multiclass
[1] "Remove cluster labels:" "19Q LOSS CNV"          
clus
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                 91 
        TCGA-A4-7287         TCGA-A4-7583         TCGA-A4-7584 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7585         TCGA-A4-7734         TCGA-A4-7828 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-7996         TCGA-A4-8098 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3471         TCGA-AL-3473 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B3-3925 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-3926         TCGA-B3-4103         TCGA-B3-4104 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B3-8121         TCGA-B9-4113         TCGA-B9-4115 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-7268         TCGA-BQ-5875 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5876         TCGA-BQ-5877         TCGA-BQ-5878 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5881 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5883         TCGA-BQ-5884 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5886         TCGA-BQ-5887 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5888         TCGA-BQ-5889         TCGA-BQ-5890 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5891         TCGA-BQ-5892         TCGA-BQ-5893 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-5894         TCGA-BQ-7044         TCGA-BQ-7045 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7046         TCGA-BQ-7048         TCGA-BQ-7049 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7050         TCGA-BQ-7051         TCGA-BQ-7053 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7055         TCGA-BQ-7056         TCGA-BQ-7058 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7059         TCGA-BQ-7060         TCGA-BQ-7061 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-BQ-7062         TCGA-DW-5560         TCGA-DW-5561 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DZ-6131 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6132         TCGA-DZ-6133         TCGA-DZ-6134 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DZ-6135         TCGA-EV-5901         TCGA-EV-5902 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6789         TCGA-G7-6790 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-G7-6796         TCGA-G7-6797         TCGA-G7-7501 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7773         TCGA-GL-7966 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HE-7128         TCGA-HE-7129         TCGA-HE-7130 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-J7-6720 
"19Q LOSS WILD-TYPE" 

Clustering(56) Variable = 21q loss
D56V1, survival
                    sevent
clus2                 0  1
  21Q LOSS CNV       11  0
  21Q LOSS WILD-TYPE 72 14
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                11                 86 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 0                 14 
$`21Q LOSS CNV`
TCGA-A4-7288 TCGA-AL-3468 TCGA-B3-3925 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5885 
       15.95        53.79         3.58         4.11        86.73        30.28 
TCGA-BQ-5890 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-G7-6796 TCGA-GL-7966 
        7.63         7.13        61.02        34.82         3.68 

$`21Q LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
        0.03         0.69         0.10        35.18         0.03         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 
        0.23         1.61         4.60         9.63        58.45        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B3-4103 
       30.31        25.08        44.61        11.05         7.33         5.88 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        4.44         4.83        50.50         0.69        10.82         3.02 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 
        0.46         1.08         0.62         6.44         1.18        19.23 
TCGA-BQ-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-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.89         2.76       123.58        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.37        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
       26.27        20.12        11.28         7.63         7.00         3.78 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.74         3.75        14.63         3.02        79.82        80.84 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       51.16        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 
       32.12        41.33        11.05        30.51        12.72        14.63 
TCGA-G7-7502 TCGA-GL-6846 
       14.07       182.73 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              3.58               0.03 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             86.73             182.73 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
            15.950             13.675 
[1] "3.6 - 86.7 (15.9)"  "0.0 - 182.7 (13.7)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "21Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "21Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV"       "21Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"21Q LOSS WILD-TYPE"       "21Q LOSS CNV" "21Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "21Q LOSS CNV" 
[1] "hr="     "8.3e+07"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          5    6
  21Q LOSS WILD-TYPE   29   64
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  FEMALE            5                 29
  MALE              6                 64
D56V4, continuous
[1] "Remove cluster labels:" "21Q LOSS CNV"          
clus
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 1                 21 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-AL-3466 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-EV-5901         TCGA-EV-5902 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-G7-6790         TCGA-G7-6793 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
                    vv
clus                 T1 T2 T3+T4
  21Q LOSS CNV        5  1     5
  21Q LOSS WILD-TYPE 53 12    28
D56V5, multiclass
       clus
vv      21Q LOSS CNV 21Q LOSS WILD-TYPE
  T1               5                 53
  T2               1                 12
  T3+T4            5                 28
                    vv
clus                 N0 N1 N2
  21Q LOSS CNV        2  1  0
  21Q LOSS WILD-TYPE 18 11  4
D56V6, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  N0            2                 18
  N1            1                 11
  N2            0                  4
                    vv
clus                 M0 M1 MX
  21Q LOSS CNV        7  0  4
  21Q LOSS WILD-TYPE 47  5 32
D56V7, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  M0            7                 47
  M1            0                  5
  MX            4                 32
                    vv
clus                  I II III IV
  21Q LOSS CNV        4  0   5  0
  21Q LOSS WILD-TYPE 49  7  19  9
D56V8, multiclass
     clus
vv    21Q LOSS CNV 21Q LOSS WILD-TYPE
  I              4                 49
  II             0                  7
  III            5                 19
  IV             0                  9

Clustering(57) Variable = 22q loss
D57V1, survival
                    sevent
clus2                 0  1
  22Q LOSS CNV       17  3
  22Q LOSS WILD-TYPE 66 11
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                20                 77 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 3                 11 
$`22Q LOSS CNV`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 
        0.03        15.95         4.60         9.63         7.33         4.11 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7050 
       86.73         8.84        26.04         7.63       123.58        61.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 
        7.13        79.82         5.85        11.05        12.72        14.63 
TCGA-G7-7502 TCGA-GL-7966 
       14.07         3.68 

$`22Q LOSS WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.69         0.10        35.18         0.03         0.89         0.23 
TCGA-A4-7996 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        1.61        58.45        53.79        13.55        30.31        25.08 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       44.61        11.05         3.58         5.88         4.44         4.83 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50         0.69        10.82         3.02         0.46         1.08 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
        0.62         6.44         1.18        19.23        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
       43.17        47.80        21.63        40.83        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25        10.82         0.95        11.97         7.89 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7051 
        2.76        48.26        96.92        93.34        44.84        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-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.78        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6132 
       24.46        13.74         3.75        14.63         3.02        80.84 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6789 
       51.16        61.02        54.87        15.48         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-6846 
       32.12        41.33        30.51        34.82       182.73 

      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              0.03               0.03 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
            123.58             182.73 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             10.34              15.48 
[1] "0.0 - 123.6 (10.3)" "0.0 - 182.7 (15.5)"
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "22Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "22Q LOSS CNV" 
        TCGA-A4-7286         TCGA-A4-7287         TCGA-A4-7288 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7732 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-7734         TCGA-A4-7915         TCGA-A4-7996 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-A4-8098         TCGA-AL-3466         TCGA-AL-3467 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3468         TCGA-AL-3471         TCGA-AL-3472 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-AL-3473         TCGA-AL-7173         TCGA-B1-5398 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B1-7332         TCGA-B3-3925         TCGA-B3-3926 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-B3-4103         TCGA-B3-4104         TCGA-B3-8121 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4113         TCGA-B9-4114         TCGA-B9-4115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-4116         TCGA-B9-4117         TCGA-B9-4617 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-B9-5155         TCGA-B9-5156         TCGA-B9-7268 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5875         TCGA-BQ-5876         TCGA-BQ-5877 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5881         TCGA-BQ-5882         TCGA-BQ-5883 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5884         TCGA-BQ-5885         TCGA-BQ-5886 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5887         TCGA-BQ-5888         TCGA-BQ-5889 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5890         TCGA-BQ-5891         TCGA-BQ-5892 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-5893         TCGA-BQ-5894         TCGA-BQ-7044 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BQ-7045         TCGA-BQ-7046         TCGA-BQ-7048 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7049         TCGA-BQ-7050         TCGA-BQ-7051 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7053         TCGA-BQ-7055         TCGA-BQ-7056 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7058         TCGA-BQ-7059         TCGA-BQ-7060 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BQ-7061         TCGA-BQ-7062         TCGA-DW-5560 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7836 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7837         TCGA-DW-7838         TCGA-DW-7839 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DW-7840         TCGA-DW-7841         TCGA-DW-7842 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6131         TCGA-DZ-6132         TCGA-DZ-6133 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DZ-6134         TCGA-DZ-6135         TCGA-EV-5901 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-G7-6789 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-GL-6846 
      "22Q LOSS CNV"       "22Q LOSS CNV" "22Q LOSS WILD-TYPE" 
        TCGA-GL-7966 
      "22Q LOSS CNV" 
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV         10   10
  22Q LOSS WILD-TYPE   24   60
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  FEMALE           10                 24
  MALE             10                 60
D57V4, continuous
                    vv
clus                 T1 T2 T3+T4
  22Q LOSS CNV        9  1    10
  22Q LOSS WILD-TYPE 49 12    23
D57V5, multiclass
       clus
vv      22Q LOSS CNV 22Q LOSS WILD-TYPE
  T1               9                 49
  T2               1                 12
  T3+T4           10                 23
                    vv
clus                 N0 N1 N2
  22Q LOSS CNV        3  4  1
  22Q LOSS WILD-TYPE 17  8  3
D57V6, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  N0            3                 17
  N1            4                  8
  N2            1                  3
                    vv
clus                 M0 M1 MX
  22Q LOSS CNV        8  2  9
  22Q LOSS WILD-TYPE 46  3 27
D57V7, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  M0            8                 46
  M1            2                  3
  MX            9                 27
                    vv
clus                  I II III IV
  22Q LOSS CNV        7  1   7  3
  22Q LOSS WILD-TYPE 46  6  17  6
D57V8, multiclass
     clus
vv    22Q LOSS CNV 22Q LOSS WILD-TYPE
  I              7                 46
  II             1                  6
  III            7                 17
  IV             3                  6

Clustering(58) Variable = Xq loss
D58V1, survival
                   sevent
clus2                0  1
  XQ LOSS CNV        3  0
  XQ LOSS WILD-TYPE 80 14
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                3                94 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                0                14 
$`XQ LOSS CNV`
TCGA-B3-3926 TCGA-B9-5155 TCGA-DW-5561 
        4.11         0.62        13.61 

$`XQ LOSS WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
        0.03         0.69        15.95         0.10        35.18         0.03 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3467 
        0.89         0.23         1.61         4.60         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 
       53.79        13.55        30.31        25.08        44.61        11.05 
TCGA-B1-7332 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        7.33         3.58         5.88         4.44         4.83        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
        0.69        10.82         3.02         0.46         1.08         6.44 
TCGA-B9-7268 TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
        1.18        86.73        19.23         8.84        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.17        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.82         7.63         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
       11.97         7.89         2.76       123.58        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.37        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-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-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.74 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        3.75        14.63         3.02        79.82        80.84        51.16 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-G7-6789 
       61.02        54.87        15.48         5.85         5.26         6.84 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       32.12        41.33        11.05        30.51        34.82        12.72 
TCGA-G7-7501 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-7966 
       14.63        14.07       182.73         3.68 

      XQ LOSS CNV XQ LOSS WILD-TYPE 
             0.62              0.03 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            13.61            182.73 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
             4.11             14.35 
[1] "0.6 - 13.6 (4.1)"   "0.0 - 182.7 (14.4)"
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966 
"XQ LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966 
"XQ LOSS WILD-TYPE" 
       TCGA-A4-7286        TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7915 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466        TCGA-AL-3467 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472        TCGA-AL-3473 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332        TCGA-B3-3925 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3926        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
      "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4113        TCGA-B9-4114        TCGA-B9-4115        TCGA-B9-4116 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-4617        TCGA-B9-5155        TCGA-B9-5156 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-5561        TCGA-DW-7834        TCGA-DW-7836 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7837        TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7841        TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6133        TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6792        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6797        TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966 
"XQ LOSS WILD-TYPE" 
[1] "hr="     "9100000"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          1    2
  XQ LOSS WILD-TYPE   33   68
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  FEMALE           1                33
  MALE             2                68
D58V4, continuous
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                1                21 
       TCGA-A4-7286        TCGA-A4-7828        TCGA-AL-3466        TCGA-DW-5560 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837        TCGA-DW-7838 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841        TCGA-DW-7842 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5901        TCGA-EV-5902        TCGA-EV-5903        TCGA-G7-6790 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6796        TCGA-G7-6797        TCGA-G7-7501 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7502 
"XQ LOSS WILD-TYPE" 
                   vv
clus                T1 T2 T3+T4
  XQ LOSS CNV        2  0     1
  XQ LOSS WILD-TYPE 56 13    32
D58V5, multiclass
       clus
vv      XQ LOSS CNV XQ LOSS WILD-TYPE
  T1              2                56
  T2              0                13
  T3+T4           1                32
                   vv
clus                N0 N1 N2
  XQ LOSS CNV        0  0  0
  XQ LOSS WILD-TYPE 20 12  4
D58V6, multiclass
                   vv
clus                M0 M1 MX
  XQ LOSS CNV        2  0  0
  XQ LOSS WILD-TYPE 52  5 36
D58V7, multiclass
[1] "Remove cluster labels:" "XQ LOSS CNV"           
clus
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                93 
       TCGA-A4-7287        TCGA-A4-7288        TCGA-A4-7583        TCGA-A4-7584 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7585        TCGA-A4-7732        TCGA-A4-7734        TCGA-A4-7828 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-A4-7915        TCGA-A4-7996        TCGA-A4-8098        TCGA-AL-3466 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3467        TCGA-AL-3468        TCGA-AL-3471        TCGA-AL-3472 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-AL-3473        TCGA-AL-7173        TCGA-B1-5398        TCGA-B1-7332 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B3-3925        TCGA-B3-4103        TCGA-B3-4104        TCGA-B3-8121 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-B9-7268        TCGA-BQ-5875        TCGA-BQ-5876        TCGA-BQ-5877 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5878        TCGA-BQ-5879        TCGA-BQ-5880        TCGA-BQ-5881 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5882        TCGA-BQ-5883        TCGA-BQ-5884        TCGA-BQ-5885 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5886        TCGA-BQ-5887        TCGA-BQ-5888        TCGA-BQ-5889 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5890        TCGA-BQ-5891        TCGA-BQ-5892        TCGA-BQ-5893 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-5894        TCGA-BQ-7044        TCGA-BQ-7045        TCGA-BQ-7046 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7048        TCGA-BQ-7049        TCGA-BQ-7050        TCGA-BQ-7051 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7053        TCGA-BQ-7055        TCGA-BQ-7056        TCGA-BQ-7058 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-BQ-7059        TCGA-BQ-7060        TCGA-BQ-7061        TCGA-BQ-7062 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-5560        TCGA-DW-7834        TCGA-DW-7836        TCGA-DW-7837 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7838        TCGA-DW-7839        TCGA-DW-7840        TCGA-DW-7841 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DW-7842        TCGA-DZ-6131        TCGA-DZ-6132        TCGA-DZ-6133 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DZ-6134        TCGA-DZ-6135        TCGA-EV-5901        TCGA-EV-5902 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-EV-5903        TCGA-G7-6789        TCGA-G7-6790        TCGA-G7-6792 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-6796        TCGA-G7-6797 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-7502        TCGA-GL-6846        TCGA-GL-7773 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-GL-7966        TCGA-HE-7128        TCGA-HE-7129        TCGA-HE-7130 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-J7-6720 
"XQ LOSS WILD-TYPE" 
                   vv
clus                 I II III IV
  XQ LOSS CNV        2  0   1  0
  XQ LOSS WILD-TYPE 51  7  23  9
D58V8, multiclass
     clus
vv    XQ LOSS CNV XQ LOSS WILD-TYPE
  I             2                51
  II            0                 7
  III           1                23
  IV            0                 9
                         V1.D                            V2 
              "Time to Death"                         "AGE" 
                           V3                            V4 
                     "GENDER" "KARNOFSKY.PERFORMANCE.SCORE" 
                           V5                            V6 
                "PATHOLOGY.T"                 "PATHOLOGY.N" 
                           V7                            V8 
        "PATHOLOGICSPREAD(M)"                 "TUMOR.STAGE" 
> q(save="no")
