
R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/159345/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/PRAD/1669681/1.GDAC_clinicalDataPicker.Finished/PRAD.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=PRAD", "-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=PRAD"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=127, in cluster file=152, common to both=123
[1] "Reduce the number of clustering variables from 80 to 20."
[1]  20 123
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4               119 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4               119 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5               118 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5               118 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7               116 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7               116 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14               109 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14               109 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11               112 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11               112 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4               119 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4               119 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11               112 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11               112 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               120 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               120 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5               118 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5               118 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36                87 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36                87 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               119 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               119 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                120 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                120 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                118 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                118 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                114 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                114 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                109 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                109 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                109 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                109 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                113 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                113 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                15                108 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                15                108 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                119 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                119 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                118 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                118 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "DAYSTOLASTKNOWNALIVE"                  
[10] "HISTOLOGICALTYPE"                      
[11] "RADIATIONS.RADIATION.REGIMENINDICATION"
[12] "NEOADJUVANTTHERAPY"                    
[13] "BATCHNUMBER"                           

Input Data has 13 rows and 123 columns.

[1] "Batch" "13"   
[1] "Last Follow UP"
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
          91          212          671           31          395          424 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
          60          731           31          395         1065          942 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
          31           62           28         1339          365           31 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
         700           31          458          731           62          395 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
         485          820          303          974         1004           91 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
         881          378          605          594          396          536 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
         532          729          244          530          229          447 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
         356          182          907         1096          737          788 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
         782          724         1061          783          849         1195 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 
        1153          842         1403          834          790          567 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
         397         1272          724          910          519          821 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 
        1490         1860          295          289          285          175 
TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
         170          191            9          169           64          131 
TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 
         167          258           79           52           70          217 
TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 
         526          284           32          923         2328         1925 
TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 
        1669         1649         1338          554         1144         1215 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 
         847         1000         1008          822          993          841 
TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
         804          101          875          851          806          846 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
         505          518          664          390          356         1442 
TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 
        1014         1109           31           51           72         2315 
TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1949         1899           NA 
Variable 1:'AGE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=110,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BATCH.NUMBER':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NEOADJUVANT.THERAPY"                   
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 123 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=28, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NEOADJUVANT.THERAPY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED     4   0
  1Q GAIN WILD-TYPE 118   1
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4               119 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 1 
$`1Q GAIN MUTATED`
TCGA-EJ-5518 TCGA-EJ-7784 TCGA-G9-6362 TCGA-G9-6499 
       39.29         5.49        27.02        36.46 

$`1Q GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        12.99 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.95        26.96         9.96        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       28.96        12.43        19.89        19.53        13.02        17.62 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       17.49        23.97         8.02        17.42         7.53        14.70 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       11.70         5.98        29.82        36.03        24.23        25.91 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 
       25.71        23.80        34.88        25.74        27.91        37.91 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       27.68        46.13        27.42        25.97        18.64        13.05 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       41.82        23.80        29.92        17.06        26.99        48.99 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15         9.70         9.50         9.37         5.75         5.59 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30         5.56         2.10         4.31         8.48 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        2.60         1.71         2.30         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       43.99        18.21        37.61        39.95        27.85        32.88 
TCGA-G9-6361 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       33.14        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-H9-7775 TCGA-HC-7230 
       12.82        11.70        47.41        33.34         1.02         1.68 
TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        2.37        65.92        64.08        62.43        66.02 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             5.49              0.30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            39.29             66.02 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            31.74             18.64 
[1] "5.5 - 39.3 (31.7)" "0.3 - 66.0 (18.6)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0    4
  1Q GAIN WILD-TYPE    5  114
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                0                 5
  YES               4               114
D1V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      0    4
  1Q GAIN WILD-TYPE    4  115
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                0                 4
  YES               4               115

Clustering(2) Variable = 3p gain mutation analysis
D2V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED     5   0
  3P GAIN WILD-TYPE 117   1
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                5               118 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 1 
$`3P GAIN MUTATED`
TCGA-CH-5761 TCGA-EJ-5497 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-G9-6363 
        0.92        13.02         2.10        17.29        32.65 

$`3P GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        12.99        15.95 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.96         9.96        32.02        33.01         2.99        28.96 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       12.43        19.89        19.53        17.62        17.49        23.97 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
        8.02        17.42         7.53        14.70        11.70         5.98 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       29.82        36.03        24.23        25.91        25.71        23.80 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 
       34.88        25.74        27.91        39.29        37.91        27.68 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       46.13        27.42        25.97        18.64        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.70         9.50         9.37         5.75         5.59         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30         5.56         4.31         5.49         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 
        1.71         2.30         7.13         9.34         1.05        30.35 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
       65.92        63.29        54.87        54.21        43.99        18.21 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       37.61        39.95        27.85        32.88        33.14        27.02 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       27.65        26.43         3.32        28.77        27.98        26.50 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       27.81        16.60        17.03        21.83        12.82        11.70 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 
       47.41        33.34        36.46         1.02         1.68         2.37 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       65.92        64.08        62.43        66.02 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.92              0.30 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            32.65             66.02 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            13.02             20.86 
[1] "0.9 - 32.6 (13.0)" "0.3 - 66.0 (20.9)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    5
  3P GAIN WILD-TYPE    5  113
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 5
  YES               5               113
D2V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      0    5
  3P GAIN WILD-TYPE    4  114
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                0                 4
  YES               5               114

Clustering(3) Variable = 3q gain mutation analysis
D3V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED     7   0
  3Q GAIN WILD-TYPE 115   1
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                7               116 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                0                 1 
$`3Q GAIN MUTATED`
TCGA-CH-5761 TCGA-CH-5788 TCGA-EJ-5497 TCGA-EJ-7782 TCGA-EJ-7792 TCGA-G9-6338 
        0.92        26.96        13.02         2.10        17.29        54.21 
TCGA-G9-6363 
       32.65 

$`3Q GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         2.04        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        12.99        15.95 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.96        32.02        33.01         2.99        28.96        12.43 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.89        19.53        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       17.42         7.53        14.70        11.70         5.98        29.82 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       36.03        24.23        25.91        25.71        23.80        34.88 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       25.74        27.91        39.29        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       27.42        25.97        18.64        13.05        41.82        23.80 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 
       29.92        17.06        26.99        48.99        61.15         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.50         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        5.56         4.31         5.49         8.48         2.60         1.71 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 
        2.30         7.13         9.34         1.05        30.35        65.92 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 
       63.29        54.87        43.99        18.21        37.61        39.95 
TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 
       27.85        32.88        33.14        27.02        27.65        26.43 
TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 
        3.32        28.77        27.98        26.50        27.81        16.60 
TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 
       17.03        21.83        12.82        11.70        47.41        33.34 
TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 
       36.46         1.02         1.68         2.37        65.92        64.08 
TCGA-HI-7170 TCGA-HI-7171 
       62.43        66.02 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.92              0.30 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            54.21             66.02 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            17.29             19.71 
[1] "0.9 - 54.2 (17.3)" "0.3 - 66.0 (19.7)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      0    7
  3Q GAIN WILD-TYPE    5  111
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                0                 5
  YES               7               111
D3V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      1    6
  3Q GAIN WILD-TYPE    3  113
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                1                 3
  YES               6               113

Clustering(4) Variable = 7p gain mutation analysis
D4V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED    14   0
  7P GAIN WILD-TYPE 108   1
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               14               109 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                0                 1 
$`7P GAIN MUTATED`
TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 
       35.01         2.04        26.96        19.89        36.03        25.97 
TCGA-EJ-5542 TCGA-EJ-7330 TCGA-EJ-7784 TCGA-EJ-7786 TCGA-EJ-7789 TCGA-G9-6366 
       17.06         6.28         5.49         2.60         2.30         3.32 
TCGA-G9-6496 TCGA-G9-6499 
       33.34        36.46 

$`7P GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        12.99        30.97         1.02 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
       15.06        24.03         2.04        12.99        15.95         9.96 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 
       32.02        33.01         2.99        28.96        12.43        19.53 
TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 
       13.02        17.62        17.49        23.97         8.02        17.42 
TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5510 
        7.53        14.70        11.70         5.98        29.82        24.23 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       25.91        25.71        23.80        34.88        25.74        27.91 
TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 
       39.29        37.91        27.68        46.13        27.42        18.64 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-7115 TCGA-EJ-7123 
       13.05        41.82        23.80        29.92        26.99        48.99 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15         9.70         9.50         9.37         5.75         5.59 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7788 
        0.30         5.56         2.10         4.31         8.48         1.71 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 
        7.13        17.29         9.34         1.05        30.35        65.92 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 
       63.29        54.87        54.21        43.99        18.21        37.61 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       39.95        27.85        32.88        33.14        27.02        32.65 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 
       27.65        26.43        28.77        27.98        26.50        27.81 
TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       16.60        17.03        21.83        12.82        11.70        47.41 
TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 
        1.02         1.68         2.37        65.92        64.08        62.43 
TCGA-HI-7171 
       66.02 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             2.04              0.30 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            36.46             66.02 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           18.475            19.530 
[1] "2.0 - 36.5 (18.5)" "0.3 - 66.0 (19.5)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      0   14
  7P GAIN WILD-TYPE    5  104
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                0                 5
  YES              14               104
D4V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      2   12
  7P GAIN WILD-TYPE    2  107
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                2                 2
  YES              12               107

Clustering(5) Variable = 7q gain mutation analysis
D5V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED    11   0
  7Q GAIN WILD-TYPE 111   1
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               11               112 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                0                 1 
$`7Q GAIN MUTATED`
TCGA-CH-5751 TCGA-EJ-5495 TCGA-EJ-5509 TCGA-EJ-5525 TCGA-EJ-5542 TCGA-EJ-7330 
       35.01        19.89        36.03        25.97        17.06         6.28 
TCGA-EJ-7784 TCGA-EJ-7789 TCGA-G9-6366 TCGA-G9-6496 TCGA-G9-6499 
        5.49         2.30         3.32        33.34        36.46 

$`7Q GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        12.99        30.97         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        12.99        15.95 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.96         9.96        32.02        33.01         2.99        28.96 
TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       12.43        19.53        13.02        17.62        17.49        23.97 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
        8.02        17.42         7.53        14.70        11.70         5.98 
TCGA-EJ-5508 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       29.82        24.23        25.91        25.71        23.80        34.88 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       25.74        27.91        39.29        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       27.42        18.64        13.05        41.82        23.80        29.92 
TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 
       26.99        48.99        61.15         9.70         9.50         9.37 
TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 
        5.75         5.59         0.30         5.56         2.10         4.31 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        8.48         2.60         1.71         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       43.99        18.21        37.61        39.95        27.85        32.88 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 
       33.14        27.02        32.65        27.65        26.43        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 
       12.82        11.70        47.41         1.02         1.68         2.37 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       65.92        64.08        62.43        66.02 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              2.3               0.3 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            36.46             66.02 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           19.890            19.085 
[1] "2.3 - 36.5 (19.9)" "0.3 - 66.0 (19.1)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      0   11
  7Q GAIN WILD-TYPE    5  107
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                0                 5
  YES              11               107
D5V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      1   10
  7Q GAIN WILD-TYPE    3  109
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                1                 3
  YES              10               109

Clustering(6) Variable = 8p gain mutation analysis
D6V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED     4   0
  8P GAIN WILD-TYPE 118   1
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                4               119 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 1 
$`8P GAIN MUTATED`
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-7784 TCGA-EJ-7789 
       25.97        18.64         5.49         2.30 

$`8P GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        12.99 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.95        26.96         9.96        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
       28.96        12.43        19.89        19.53        13.02        17.62 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       17.49        23.97         8.02        17.42         7.53        14.70 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       11.70         5.98        29.82        36.03        24.23        25.91 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       25.71        23.80        34.88        25.74        27.91        39.29 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5527 TCGA-EJ-5530 
       37.91        27.68        46.13        27.42        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.70         9.50         9.37         5.75         5.59         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 TCGA-EJ-7786 
        0.30         5.56         2.10         4.31         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 
        1.71         7.13        17.29         9.34         1.05        30.35 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
       65.92        63.29        54.87        54.21        43.99        18.21 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       37.61        39.95        27.85        32.88        33.14        27.02 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       32.65        27.65        26.43         3.32        28.77        27.98 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       26.50        27.81        16.60        17.03        21.83        12.82 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 
       11.70        47.41        33.34        36.46         1.02         1.68 
TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        2.37        65.92        64.08        62.43        66.02 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
              2.3               0.3 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            25.97             66.02 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           12.065            19.890 
[1] "2.3 - 26.0 (12.1)" "0.3 - 66.0 (19.9)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    4
  8P GAIN WILD-TYPE    5  114
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                0                 5
  YES               4               114
D6V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      0    4
  8P GAIN WILD-TYPE    4  115
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                0                 4
  YES               4               115

Clustering(7) Variable = 8q gain mutation analysis
D7V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    11   0
  8Q GAIN WILD-TYPE 111   1
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               11               112 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 1 
$`8Q GAIN MUTATED`
TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5511 TCGA-EJ-5525 TCGA-EJ-5526 
       22.06        35.01         0.92        25.91        25.97        18.64 
TCGA-EJ-7123 TCGA-EJ-7784 TCGA-EJ-7789 TCGA-G9-6366 TCGA-G9-6499 
       48.99         5.49         2.30         3.32        36.46 

$`8Q GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.94         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        12.99        30.97         1.02         2.04 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        12.99        15.95        26.96         9.96 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        28.96        12.43        19.89 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.53        13.02        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       17.42         7.53        14.70        11.70         5.98        29.82 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 
       36.03        24.23        25.71        23.80        34.88        25.74 
TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       27.91        39.29        37.91        27.68        46.13        27.42 
TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 
       13.05        41.82        23.80        29.92        17.06        26.99 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15         9.70         9.50         9.37         5.75         5.59 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7785 
        6.28         0.30         5.56         2.10         4.31         8.48 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        2.60         1.71         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6367 TCGA-G9-6369 
       27.02        32.65        27.65        26.43        28.77        27.98 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 
       26.50        27.81        16.60        17.03        21.83        12.82 
TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 
       11.70        47.41        33.34         1.02         1.68         2.37 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       65.92        64.08        62.43        66.02 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.92              0.30 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            48.99             66.02 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            22.06             18.87 
[1] "0.9 - 49.0 (22.1)" "0.3 - 66.0 (18.9)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      0   11
  8Q GAIN WILD-TYPE    5  107
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                0                 5
  YES              11               107
D7V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1   10
  8Q GAIN WILD-TYPE    3  109
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1                 3
  YES              10               109

Clustering(8) Variable = 9q gain mutation analysis
D8V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED     3   0
  9Q GAIN WILD-TYPE 119   1
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3               120 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                 1 
$`9Q GAIN MUTATED`
TCGA-EJ-5496 TCGA-EJ-7789 TCGA-G9-6373 
       19.53         2.30        16.60 

$`9Q GAIN WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        12.99 
TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 
       15.95        26.96         9.96        32.02        33.01         2.99 
TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       28.96        12.43        19.89        13.02        17.62        17.49 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       23.97         8.02        17.42         7.53        14.70        11.70 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
        5.98        29.82        36.03        24.23        25.91        25.71 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       23.80        34.88        25.74        27.91        39.29        37.91 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       27.68        46.13        27.42        25.97        18.64        13.05 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       41.82        23.80        29.92        17.06        26.99        48.99 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15         9.70         9.50         9.37         5.75         5.59 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30         5.56         2.10         4.31         5.49 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        8.48         2.60         1.71         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       43.99        18.21        37.61        39.95        27.85        32.88 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 
       33.14        27.02        32.65        27.65        26.43         3.32 
TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 
       28.77        27.98        26.50        27.81        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 
       12.82        11.70        47.41        33.34        36.46         1.02 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.68         2.37        65.92        64.08        62.43        66.02 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
              2.3               0.3 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            19.53             66.02 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            16.60             20.86 
[1] "2.3 - 19.5 (16.6)" "0.3 - 66.0 (20.9)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE    5  115
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                 5
  YES               3               115
D8V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      0    3
  9Q GAIN WILD-TYPE    4  116
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                0                 4
  YES               3               116

Clustering(9) Variable = 6q loss mutation analysis
D9V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED     5   0
  6Q LOSS WILD-TYPE 117   1
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                5               118 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                0                 1 
$`6Q LOSS MUTATED`
TCGA-CH-5753 TCGA-EJ-5511 TCGA-EJ-5518 TCGA-EJ-7782 TCGA-EJ-7786 
        1.02        25.91        39.29         2.10         2.60 

$`6Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        12.99        15.95 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.96         9.96        32.02        33.01         2.99        28.96 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       12.43        19.89        19.53        13.02        17.62        17.49 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       23.97         8.02        17.42         7.53        14.70        11.70 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5512 TCGA-EJ-5514 
        5.98        29.82        36.03        24.23        25.71        23.80 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       34.88        25.74        27.91        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       27.42        25.97        18.64        13.05        41.82        23.80 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 
       29.92        17.06        26.99        48.99        61.15         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.50         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7788 TCGA-EJ-7789 
        5.56         4.31         5.49         8.48         1.71         2.30 
TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 
        7.13        17.29         9.34         1.05        30.35        65.92 
TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 
       63.29        54.87        54.21        43.99        18.21        37.61 
TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6363 
       39.95        27.85        32.88        33.14        27.02        32.65 
TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       27.65        26.43         3.32        28.77        27.98        26.50 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       27.81        16.60        17.03        21.83        12.82        11.70 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 
       47.41        33.34        36.46         1.02         1.68         2.37 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       65.92        64.08        62.43        66.02 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             1.02              0.30 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            39.29             66.02 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             2.60             19.71 
[1] "1.0 - 39.3 (2.6)"  "0.3 - 66.0 (19.7)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    5
  6Q LOSS WILD-TYPE    5  113
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 5
  YES               5               113
D9V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      0    5
  6Q LOSS WILD-TYPE    4  114
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                0                 4
  YES               5               114

Clustering(10) Variable = 8p loss mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   35  1
  8P LOSS WILD-TYPE 87  0
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               36                87 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 0 
$`8P LOSS MUTATED`
TCGA-CH-5739 TCGA-CH-5744 TCGA-CH-5751 TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5765 
       22.06         1.97        35.01         1.02         2.04        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5788 TCGA-CH-5790 TCGA-CH-5791 TCGA-EJ-5499 
        1.02        15.06        26.96        32.02        33.01        17.49 
TCGA-EJ-5501 TCGA-EJ-5507 TCGA-EJ-5518 TCGA-EJ-5530 TCGA-EJ-5532 TCGA-EJ-7115 
       23.97         5.98        39.29        41.82        29.92        26.99 
TCGA-EJ-7314 TCGA-EJ-7781 TCGA-EJ-7783 TCGA-EJ-7788 TCGA-FC-7708 TCGA-G9-6332 
        9.70         5.56         4.31         1.71         1.05        65.92 
TCGA-G9-6333 TCGA-G9-6342 TCGA-G9-6361 TCGA-G9-6364 TCGA-G9-6373 TCGA-G9-6384 
       63.29        43.99        33.14        27.65        16.60        12.82 
TCGA-G9-6494 TCGA-G9-6496 TCGA-H9-7775 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
       47.41        33.34         1.02        65.92        62.43        66.02 

$`8P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5746 
        2.99         6.97         1.02        12.99        13.94        24.03 
TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 
        1.02        12.99        30.97         0.92        44.02        12.00 
TCGA-CH-5764 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 
        1.02        24.03         2.04        12.99        15.95         9.96 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 
        2.99        28.96        12.43        19.89        19.53        13.02 
TCGA-EJ-5498 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       17.62         8.02        17.42         7.53        14.70        11.70 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       29.82        36.03        24.23        25.91        25.71        23.80 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       34.88        25.74        27.91        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5531 TCGA-EJ-5542 
       27.42        25.97        18.64        13.05        23.80        17.06 
TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       48.99        61.15         9.50         9.37         5.75         5.59 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7782 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        6.28         0.30         2.10         5.49         8.48         2.60 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-G9-6329 TCGA-G9-6336 
        2.30         7.13        17.29         9.34        30.35        54.87 
TCGA-G9-6338 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       54.21        18.21        37.61        39.95        27.85        32.88 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       27.02        32.65        26.43         3.32        28.77        27.98 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6385 TCGA-G9-6499 
       26.50        27.81        17.03        21.83        11.70        36.46 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7169 
        1.68         2.37        64.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.02              0.30 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            66.02             64.08 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           25.465            17.620 
[1] "1.0 - 66.0 (25.5)" "0.3 - 64.1 (17.6)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
[1] "hr=" "1"  
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      0   36
  8P LOSS WILD-TYPE    5   82
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                0                 5
  YES              36                82
D10V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      2   34
  8P LOSS WILD-TYPE    2   85
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                2                 2
  YES              34                85

Clustering(11) Variable = 8q loss mutation analysis
D11V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     4   0
  8Q LOSS WILD-TYPE 118   1
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4               119 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                0                 1 
$`8Q LOSS MUTATED`
TCGA-CH-5754 TCGA-CH-5766 TCGA-EJ-5507 TCGA-HI-7168 
        2.04         1.02         5.98        65.92 

$`8Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        1.02         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        12.99        15.95        26.96 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.96        32.02        33.01         2.99        28.96        12.43 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       19.89        19.53        13.02        17.62        17.49        23.97 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 
        8.02        17.42         7.53        14.70        11.70        29.82 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       36.03        24.23        25.91        25.71        23.80        34.88 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       25.74        27.91        39.29        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       27.42        25.97        18.64        13.05        41.82        23.80 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 
       29.92        17.06        26.99        48.99        61.15         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.50         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        5.56         2.10         4.31         5.49         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        1.71         2.30         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 
       12.82        11.70        47.41        33.34        36.46         1.02 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.68         2.37        64.08        62.43        66.02 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.02              0.30 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            65.92             66.02 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             4.01             19.89 
[1] "1.0 - 65.9 (4.0)"  "0.3 - 66.0 (19.9)"
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5737        TCGA-CH-5738        TCGA-CH-5739        TCGA-CH-5740 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5741        TCGA-CH-5743        TCGA-CH-5744        TCGA-CH-5746 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5748        TCGA-CH-5750        TCGA-CH-5751        TCGA-CH-5752 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5753        TCGA-CH-5754        TCGA-CH-5761        TCGA-CH-5762 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5763        TCGA-CH-5764        TCGA-CH-5765        TCGA-CH-5766 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-CH-5767        TCGA-CH-5768        TCGA-CH-5769        TCGA-CH-5771 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5772        TCGA-CH-5788        TCGA-CH-5789        TCGA-CH-5790 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CH-5791        TCGA-CH-5792        TCGA-CH-5794        TCGA-EJ-5494 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5495        TCGA-EJ-5496        TCGA-EJ-5497        TCGA-EJ-5498 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5499        TCGA-EJ-5501        TCGA-EJ-5502        TCGA-EJ-5503 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5504        TCGA-EJ-5505        TCGA-EJ-5506        TCGA-EJ-5507 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-EJ-5508        TCGA-EJ-5509        TCGA-EJ-5510        TCGA-EJ-5511 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5512        TCGA-EJ-5514        TCGA-EJ-5515        TCGA-EJ-5516 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5517        TCGA-EJ-5518        TCGA-EJ-5519        TCGA-EJ-5521 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5522        TCGA-EJ-5524        TCGA-EJ-5525        TCGA-EJ-5526 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5527        TCGA-EJ-5530        TCGA-EJ-5531        TCGA-EJ-5532 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-5542        TCGA-EJ-7115        TCGA-EJ-7123        TCGA-EJ-7125 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7314        TCGA-EJ-7315        TCGA-EJ-7317        TCGA-EJ-7327 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7328        TCGA-EJ-7330        TCGA-EJ-7331        TCGA-EJ-7781 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7782        TCGA-EJ-7783        TCGA-EJ-7784        TCGA-EJ-7785 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7786        TCGA-EJ-7788        TCGA-EJ-7789        TCGA-EJ-7791 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EJ-7792        TCGA-EJ-7794        TCGA-FC-7708        TCGA-G9-6329 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6332        TCGA-G9-6333        TCGA-G9-6336        TCGA-G9-6338 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6342        TCGA-G9-6343        TCGA-G9-6348        TCGA-G9-6351 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6353        TCGA-G9-6356        TCGA-G9-6361        TCGA-G9-6362 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6363        TCGA-G9-6364        TCGA-G9-6365        TCGA-G9-6366 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6367        TCGA-G9-6369        TCGA-G9-6370        TCGA-G9-6371 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6373        TCGA-G9-6377        TCGA-G9-6378        TCGA-G9-6384 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G9-6385        TCGA-G9-6494        TCGA-G9-6496        TCGA-G9-6499 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-H9-7775        TCGA-HC-7230        TCGA-HC-7231        TCGA-HI-7168 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-HI-7169        TCGA-HI-7170        TCGA-HI-7171 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE    5  114
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 5
  YES               4               114
D11V4, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0    4
  8Q LOSS WILD-TYPE    4  115
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 4
  YES               4               115

Clustering(12) Variable = 10p loss mutation analysis
D12V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED     3   0
  10P LOSS WILD-TYPE 119   1
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                120 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  1 
$`10P LOSS MUTATED`
TCGA-CH-5788 TCGA-EJ-5518 TCGA-G9-6363 
       26.96        39.29        32.65 

$`10P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        12.99 
TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       15.95         9.96        32.02        33.01         2.99        28.96 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       12.43        19.89        19.53        13.02        17.62        17.49 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       23.97         8.02        17.42         7.53        14.70        11.70 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
        5.98        29.82        36.03        24.23        25.91        25.71 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5519 TCGA-EJ-5521 
       23.80        34.88        25.74        27.91        37.91        27.68 
TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       46.13        27.42        25.97        18.64        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.70         9.50         9.37         5.75         5.59         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30         5.56         2.10         4.31         5.49         8.48 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        2.60         1.71         2.30         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 
       43.99        18.21        37.61        39.95        27.85        32.88 
TCGA-G9-6361 TCGA-G9-6362 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       33.14        27.02        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 
       12.82        11.70        47.41        33.34        36.46         1.02 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.68         2.37        65.92        64.08        62.43        66.02 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             26.96               0.30 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             39.29              66.02 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            32.650             18.425 
[1] "27.0 - 39.3 (32.6)" "0.3 - 66.0 (18.4)" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D12V2, continuous
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    3
  10P LOSS WILD-TYPE    5  115
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 0                  5
  YES                3                115
D12V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      1    2
  10P LOSS WILD-TYPE    3  117
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 1                  3
  YES                2                117

Clustering(13) Variable = 12p loss mutation analysis
D13V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     5   0
  12P LOSS WILD-TYPE 117   1
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                118 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                  1 
$`12P LOSS MUTATED`
TCGA-CH-5744 TCGA-CH-5766 TCGA-EJ-5519 TCGA-EJ-5522 TCGA-G9-6364 
        1.97         1.02        37.91        46.13        27.65 

$`12P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        12.99        35.01        30.97         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        12.99        15.95        26.96 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.96        32.02        33.01         2.99        28.96        12.43 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       19.89        19.53        13.02        17.62        17.49        23.97 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
        8.02        17.42         7.53        14.70        11.70         5.98 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 
       29.82        36.03        24.23        25.91        25.71        23.80 
TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5524 
       34.88        25.74        27.91        39.29        27.68        27.42 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       25.97        18.64        13.05        41.82        23.80        29.92 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 
       17.06        26.99        48.99        61.15         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
        9.37         5.75         5.59         6.28         0.30         5.56 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        2.10         4.31         5.49         8.48         2.60         1.71 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 
        2.30         7.13        17.29         9.34         1.05        30.35 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
       65.92        63.29        54.87        54.21        43.99        18.21 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       37.61        39.95        27.85        32.88        33.14        27.02 
TCGA-G9-6363 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 TCGA-G9-6370 
       32.65        26.43         3.32        28.77        27.98        26.50 
TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       27.81        16.60        17.03        21.83        12.82        11.70 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 
       47.41        33.34        36.46         1.02         1.68         2.37 
TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
       65.92        64.08        62.43        66.02 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.02               0.30 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             46.13              66.02 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            27.650             19.085 
[1] "1.0 - 46.1 (27.6)" "0.3 - 66.0 (19.1)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D13V2, continuous
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    5
  12P LOSS WILD-TYPE    5  113
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  5
  YES                5                113
D13V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    5
  12P LOSS WILD-TYPE    4  114
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  4
  YES                5                114

Clustering(14) Variable = 13q loss mutation analysis
D14V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     9   0
  13Q LOSS WILD-TYPE 113   1
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 9                114 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  1 
$`13Q LOSS MUTATED`
TCGA-CH-5740 TCGA-CH-5788 TCGA-EJ-5495 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5516 
        1.02        26.96        19.89         7.53         5.98        25.74 
TCGA-EJ-5521 TCGA-EJ-5525 TCGA-EJ-7786 
       27.68        25.97         2.60 

$`13Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97        22.06        12.99        13.94         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 TCGA-CH-5753 
       24.03         1.02        12.99        35.01        30.97         1.02 
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 
        2.04         0.92        44.02        12.00         1.02        23.01 
TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 
        1.02        15.06        24.03         2.04        12.99        15.95 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.96        32.02        33.01         2.99        28.96        12.43 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.53        13.02        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       17.42        14.70        11.70        29.82        36.03        24.23 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5517 TCGA-EJ-5518 
       25.91        25.71        23.80        34.88        27.91        39.29 
TCGA-EJ-5519 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       37.91        46.13        27.42        18.64        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.70         9.50         9.37         5.75         5.59         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30         5.56         2.10         4.31         5.49         8.48 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        1.71         2.30         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 
       12.82        11.70        47.41        33.34        36.46         1.02 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        1.68         2.37        65.92        64.08        62.43        66.02 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              1.02               0.30 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             27.68              66.02 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            19.890             19.085 
[1] "1.0 - 27.7 (19.9)" "0.3 - 66.0 (19.1)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1"  
D14V2, continuous
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    9
  13Q LOSS WILD-TYPE    5  109
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  5
  YES                9                109
D14V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      1    8
  13Q LOSS WILD-TYPE    3  111
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 1                  3
  YES                8                111

Clustering(15) Variable = 16q loss mutation analysis
D15V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    13   1
  16Q LOSS WILD-TYPE 109   0
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                109 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                  0 
$`16Q LOSS MUTATED`
TCGA-CH-5739 TCGA-CH-5751 TCGA-CH-5764 TCGA-CH-5788 TCGA-CH-5791 TCGA-EJ-5495 
       22.06        35.01         1.02        26.96        33.01        19.89 
TCGA-EJ-5525 TCGA-EJ-7789 TCGA-G9-6343 TCGA-G9-6362 TCGA-G9-6384 TCGA-G9-6496 
       25.97         2.30        18.21        27.02        12.82        33.34 
TCGA-HI-7168 TCGA-HI-7171 
       65.92        66.02 

$`16Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 TCGA-CH-5744 
        2.99         6.97         1.02        12.99        13.94         1.97 
TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 TCGA-CH-5754 
       24.03         1.02        12.99        30.97         1.02         2.04 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
        0.92        44.02        12.00        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5789 TCGA-CH-5790 
       24.03         2.04        12.99        15.95         9.96        32.02 
TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 
        2.99        28.96        12.43        19.53        13.02        17.62 
TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 
       17.49        23.97         8.02        17.42         7.53        14.70 
TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 
       11.70         5.98        29.82        36.03        24.23        25.91 
TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       25.71        23.80        34.88        25.74        27.91        39.29 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5526 TCGA-EJ-5527 
       37.91        27.68        46.13        27.42        18.64        13.05 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 
       41.82        23.80        29.92        17.06        26.99        48.99 
TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 
       61.15         9.70         9.50         9.37         5.75         5.59 
TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 
        6.28         0.30         5.56         2.10         4.31         5.49 
TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        8.48         2.60         1.71         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       43.99        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       32.65        27.65        26.43         3.32        28.77        27.98 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 TCGA-G9-6385 
       26.50        27.81        16.60        17.03        21.83        11.70 
TCGA-G9-6494 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7169 
       47.41        36.46         1.02         1.68         2.37        64.08 
TCGA-HI-7170 
       62.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              1.02               0.30 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             66.02              65.92 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            26.465             17.490 
[1] "1.0 - 66.0 (26.5)" "0.3 - 65.9 (17.5)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
[1] "hr=" "1"  
D15V2, continuous
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   14
  16Q LOSS WILD-TYPE    5  104
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 0                  5
  YES               14                104
D15V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      2   12
  16Q LOSS WILD-TYPE    2  107
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 2                  2
  YES               12                107

Clustering(16) Variable = 17p loss mutation analysis
D16V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    14   0
  17P LOSS WILD-TYPE 108   1
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                109 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  1 
$`17P LOSS MUTATED`
TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5790 TCGA-EJ-5507 TCGA-EJ-5514 TCGA-EJ-5519 
        2.04         0.92        32.02         5.98        23.80        37.91 
TCGA-EJ-5521 TCGA-EJ-5526 TCGA-EJ-7315 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6494 
       27.68        18.64         9.50        16.60        17.03        47.41 
TCGA-HC-7230 TCGA-HI-7168 
        1.68        65.92 

$`17P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        1.02        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        12.99        15.95        26.96 
TCGA-CH-5789 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
        9.96        33.01         2.99        28.96        12.43        19.89 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.53        13.02        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 
       17.42         7.53        14.70        11.70        29.82        36.03 
TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 
       24.23        25.91        25.71        34.88        25.74        27.91 
TCGA-EJ-5518 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5527 TCGA-EJ-5530 
       39.29        46.13        27.42        25.97        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.70         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        5.56         2.10         4.31         5.49         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        1.71         2.30         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       27.98        26.50        27.81        21.83        12.82        11.70 
TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7231 TCGA-HI-7169 TCGA-HI-7170 
       33.34        36.46         1.02         2.37        64.08        62.43 
TCGA-HI-7171 
       66.02 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.92               0.30 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             65.92              66.02 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            17.835             19.890 
[1] "0.9 - 65.9 (17.8)" "0.3 - 66.0 (19.9)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   14
  17P LOSS WILD-TYPE    5  104
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 0                  5
  YES               14                104
D16V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      0   14
  17P LOSS WILD-TYPE    4  105
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 0                  4
  YES               14                105

Clustering(17) Variable = 18p loss mutation analysis
D17V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED     9   1
  18P LOSS WILD-TYPE 113   0
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                10                113 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  0 
$`18P LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5761 TCGA-EJ-5514 TCGA-EJ-5519 TCGA-G9-6373 TCGA-G9-6377 
       35.01         0.92        23.80        37.91        16.60        17.03 
TCGA-HC-7230 TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
        1.68        65.92        62.43        66.02 

$`18P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        12.99        30.97         1.02 
TCGA-CH-5754 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        2.04        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 
       15.06        24.03         2.04        12.99        15.95        26.96 
TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 
        9.96        32.02        33.01         2.99        28.96        12.43 
TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 
       19.89        19.53        13.02        17.62        17.49        23.97 
TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 
        8.02        17.42         7.53        14.70        11.70         5.98 
TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 
       29.82        36.03        24.23        25.91        25.71        34.88 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 
       25.74        27.91        39.29        27.68        46.13        27.42 
TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5532 
       25.97        18.64        13.05        41.82        23.80        29.92 
TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 TCGA-EJ-7315 
       17.06        26.99        48.99        61.15         9.70         9.50 
TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 TCGA-EJ-7781 
        9.37         5.75         5.59         6.28         0.30         5.56 
TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 TCGA-EJ-7788 
        2.10         4.31         5.49         8.48         2.60         1.71 
TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 TCGA-G9-6329 
        2.30         7.13        17.29         9.34         1.05        30.35 
TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 TCGA-G9-6343 
       65.92        63.29        54.87        54.21        43.99        18.21 
TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 TCGA-G9-6362 
       37.61        39.95        27.85        32.88        33.14        27.02 
TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 TCGA-G9-6369 
       32.65        27.65        26.43         3.32        28.77        27.98 
TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 
       26.50        27.81        21.83        12.82        11.70        47.41 
TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7231 TCGA-HI-7169 
       33.34        36.46         1.02         2.37        64.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.92               0.30 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             66.02              65.92 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            29.405             18.640 
[1] "0.9 - 66.0 (29.4)" "0.3 - 65.9 (18.6)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18P LOSS MUTATED"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED"   "18P LOSS MUTATED" 
[1] "hr=" "1"  
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      0   10
  18P LOSS WILD-TYPE    5  108
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 0                  5
  YES               10                108
D17V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    9
  18P LOSS WILD-TYPE    3  110
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                  3
  YES                9                110

Clustering(18) Variable = 18q loss mutation analysis
D18V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    14   1
  18Q LOSS WILD-TYPE 108   0
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                15                108 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  0 
$`18Q LOSS MUTATED`
TCGA-CH-5751 TCGA-CH-5754 TCGA-CH-5761 TCGA-EJ-5504 TCGA-EJ-5507 TCGA-EJ-5514 
       35.01         2.04         0.92         7.53         5.98        23.80 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-G9-6348 TCGA-G9-6373 TCGA-G9-6377 TCGA-HC-7230 
       27.42        25.97        37.61        16.60        17.03         1.68 
TCGA-HI-7168 TCGA-HI-7170 TCGA-HI-7171 
       65.92        62.43        66.02 

$`18Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5752 TCGA-CH-5753 
        1.97        24.03         1.02        12.99        30.97         1.02 
TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 
       44.02        12.00         1.02        23.01         1.02        15.06 
TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5772 TCGA-CH-5788 TCGA-CH-5789 
       24.03         2.04        12.99        15.95        26.96         9.96 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        28.96        12.43        19.89 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.53        13.02        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 
       17.42        14.70        11.70        29.82        36.03        24.23 
TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 
       25.91        25.71        34.88        25.74        27.91        39.29 
TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 
       37.91        27.68        46.13        18.64        13.05        41.82 
TCGA-EJ-5531 TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       23.80        29.92        17.06        26.99        48.99        61.15 
TCGA-EJ-7314 TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 
        9.70         9.50         9.37         5.75         5.59         6.28 
TCGA-EJ-7331 TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 
        0.30         5.56         2.10         4.31         5.49         8.48 
TCGA-EJ-7786 TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 
        2.60         1.71         2.30         7.13        17.29         9.34 
TCGA-FC-7708 TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 
        1.05        30.35        65.92        63.29        54.87        54.21 
TCGA-G9-6342 TCGA-G9-6343 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       43.99        18.21        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6378 TCGA-G9-6384 TCGA-G9-6385 
       27.98        26.50        27.81        21.83        12.82        11.70 
TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7231 TCGA-HI-7169 
       47.41        33.34        36.46         1.02         2.37        64.08 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.92               0.30 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             66.02              65.92 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            23.800             19.085 
[1] "0.9 - 66.0 (23.8)" "0.3 - 65.9 (19.1)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      0   15
  18Q LOSS WILD-TYPE    5  103
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 0                  5
  YES               15                103
D18V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1   14
  18Q LOSS WILD-TYPE    3  105
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  3
  YES               14                105

Clustering(19) Variable = 20p loss mutation analysis
D19V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     4   0
  20P LOSS WILD-TYPE 118   1
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 4                119 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 0                  1 
$`20P LOSS MUTATED`
TCGA-CH-5772 TCGA-EJ-5532 TCGA-EJ-7314 TCGA-G9-6494 
       15.95        29.92         9.70        47.41 

$`20P LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 
        1.02         2.04         0.92        44.02        12.00         1.02 
TCGA-CH-5765 TCGA-CH-5766 TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 
       23.01         1.02        15.06        24.03         2.04        12.99 
TCGA-CH-5788 TCGA-CH-5789 TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 
       26.96         9.96        32.02        33.01         2.99        28.96 
TCGA-EJ-5494 TCGA-EJ-5495 TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 
       12.43        19.89        19.53        13.02        17.62        17.49 
TCGA-EJ-5501 TCGA-EJ-5502 TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 
       23.97         8.02        17.42         7.53        14.70        11.70 
TCGA-EJ-5507 TCGA-EJ-5508 TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 
        5.98        29.82        36.03        24.23        25.91        25.71 
TCGA-EJ-5514 TCGA-EJ-5515 TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 
       23.80        34.88        25.74        27.91        39.29        37.91 
TCGA-EJ-5521 TCGA-EJ-5522 TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 
       27.68        46.13        27.42        25.97        18.64        13.05 
TCGA-EJ-5530 TCGA-EJ-5531 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 
       41.82        23.80        17.06        26.99        48.99        61.15 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.50         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        5.56         2.10         4.31         5.49         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        1.71         2.30         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 TCGA-HC-7230 
       12.82        11.70        33.34        36.46         1.02         1.68 
TCGA-HC-7231 TCGA-HI-7168 TCGA-HI-7169 TCGA-HI-7170 TCGA-HI-7171 
        2.37        65.92        64.08        62.43        66.02 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
               9.7                0.3 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             47.41              66.02 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
            22.935             19.530 
[1] "9.7 - 47.4 (22.9)" "0.3 - 66.0 (19.5)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    3
  20P LOSS WILD-TYPE    4  115
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 1                  4
  YES                3                115
D19V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    4
  20P LOSS WILD-TYPE    4  115
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  4
  YES                4                115

Clustering(20) Variable = 22q loss mutation analysis
D20V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED     4   1
  22Q LOSS WILD-TYPE 118   0
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 5                118 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 1                  0 
$`22Q LOSS MUTATED`
TCGA-CH-5753 TCGA-CH-5754 TCGA-CH-5772 TCGA-HI-7168 TCGA-HI-7171 
        1.02         2.04        15.95        65.92        66.02 

$`22Q LOSS WILD-TYPE`
TCGA-CH-5737 TCGA-CH-5738 TCGA-CH-5739 TCGA-CH-5740 TCGA-CH-5741 TCGA-CH-5743 
        2.99         6.97        22.06         1.02        12.99        13.94 
TCGA-CH-5744 TCGA-CH-5746 TCGA-CH-5748 TCGA-CH-5750 TCGA-CH-5751 TCGA-CH-5752 
        1.97        24.03         1.02        12.99        35.01        30.97 
TCGA-CH-5761 TCGA-CH-5762 TCGA-CH-5763 TCGA-CH-5764 TCGA-CH-5765 TCGA-CH-5766 
        0.92        44.02        12.00         1.02        23.01         1.02 
TCGA-CH-5767 TCGA-CH-5768 TCGA-CH-5769 TCGA-CH-5771 TCGA-CH-5788 TCGA-CH-5789 
       15.06        24.03         2.04        12.99        26.96         9.96 
TCGA-CH-5790 TCGA-CH-5791 TCGA-CH-5792 TCGA-CH-5794 TCGA-EJ-5494 TCGA-EJ-5495 
       32.02        33.01         2.99        28.96        12.43        19.89 
TCGA-EJ-5496 TCGA-EJ-5497 TCGA-EJ-5498 TCGA-EJ-5499 TCGA-EJ-5501 TCGA-EJ-5502 
       19.53        13.02        17.62        17.49        23.97         8.02 
TCGA-EJ-5503 TCGA-EJ-5504 TCGA-EJ-5505 TCGA-EJ-5506 TCGA-EJ-5507 TCGA-EJ-5508 
       17.42         7.53        14.70        11.70         5.98        29.82 
TCGA-EJ-5509 TCGA-EJ-5510 TCGA-EJ-5511 TCGA-EJ-5512 TCGA-EJ-5514 TCGA-EJ-5515 
       36.03        24.23        25.91        25.71        23.80        34.88 
TCGA-EJ-5516 TCGA-EJ-5517 TCGA-EJ-5518 TCGA-EJ-5519 TCGA-EJ-5521 TCGA-EJ-5522 
       25.74        27.91        39.29        37.91        27.68        46.13 
TCGA-EJ-5524 TCGA-EJ-5525 TCGA-EJ-5526 TCGA-EJ-5527 TCGA-EJ-5530 TCGA-EJ-5531 
       27.42        25.97        18.64        13.05        41.82        23.80 
TCGA-EJ-5532 TCGA-EJ-5542 TCGA-EJ-7115 TCGA-EJ-7123 TCGA-EJ-7125 TCGA-EJ-7314 
       29.92        17.06        26.99        48.99        61.15         9.70 
TCGA-EJ-7315 TCGA-EJ-7317 TCGA-EJ-7327 TCGA-EJ-7328 TCGA-EJ-7330 TCGA-EJ-7331 
        9.50         9.37         5.75         5.59         6.28         0.30 
TCGA-EJ-7781 TCGA-EJ-7782 TCGA-EJ-7783 TCGA-EJ-7784 TCGA-EJ-7785 TCGA-EJ-7786 
        5.56         2.10         4.31         5.49         8.48         2.60 
TCGA-EJ-7788 TCGA-EJ-7789 TCGA-EJ-7791 TCGA-EJ-7792 TCGA-EJ-7794 TCGA-FC-7708 
        1.71         2.30         7.13        17.29         9.34         1.05 
TCGA-G9-6329 TCGA-G9-6332 TCGA-G9-6333 TCGA-G9-6336 TCGA-G9-6338 TCGA-G9-6342 
       30.35        65.92        63.29        54.87        54.21        43.99 
TCGA-G9-6343 TCGA-G9-6348 TCGA-G9-6351 TCGA-G9-6353 TCGA-G9-6356 TCGA-G9-6361 
       18.21        37.61        39.95        27.85        32.88        33.14 
TCGA-G9-6362 TCGA-G9-6363 TCGA-G9-6364 TCGA-G9-6365 TCGA-G9-6366 TCGA-G9-6367 
       27.02        32.65        27.65        26.43         3.32        28.77 
TCGA-G9-6369 TCGA-G9-6370 TCGA-G9-6371 TCGA-G9-6373 TCGA-G9-6377 TCGA-G9-6378 
       27.98        26.50        27.81        16.60        17.03        21.83 
TCGA-G9-6384 TCGA-G9-6385 TCGA-G9-6494 TCGA-G9-6496 TCGA-G9-6499 TCGA-H9-7775 
       12.82        11.70        47.41        33.34        36.46         1.02 
TCGA-HC-7230 TCGA-HC-7231 TCGA-HI-7169 TCGA-HI-7170 
        1.68         2.37        64.08        62.43 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1.02               0.30 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             66.02              65.92 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             15.95              19.71 
[1] "1.0 - 66.0 (15.9)" "0.3 - 65.9 (19.7)"
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-CH-5737         TCGA-CH-5738         TCGA-CH-5739 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5740         TCGA-CH-5741         TCGA-CH-5743 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5744         TCGA-CH-5746         TCGA-CH-5748 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5750         TCGA-CH-5751         TCGA-CH-5752 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5753         TCGA-CH-5754         TCGA-CH-5761 
  "22Q LOSS MUTATED"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5762         TCGA-CH-5763         TCGA-CH-5764 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5765         TCGA-CH-5766         TCGA-CH-5767 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5768         TCGA-CH-5769         TCGA-CH-5771 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5772         TCGA-CH-5788         TCGA-CH-5789 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5790         TCGA-CH-5791         TCGA-CH-5792 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CH-5794         TCGA-EJ-5494         TCGA-EJ-5495 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5496         TCGA-EJ-5497         TCGA-EJ-5498 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5499         TCGA-EJ-5501         TCGA-EJ-5502 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5503         TCGA-EJ-5504         TCGA-EJ-5505 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5506         TCGA-EJ-5507         TCGA-EJ-5508 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5509         TCGA-EJ-5510         TCGA-EJ-5511 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5512         TCGA-EJ-5514         TCGA-EJ-5515 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5516         TCGA-EJ-5517         TCGA-EJ-5518 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5519         TCGA-EJ-5521         TCGA-EJ-5522 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5524         TCGA-EJ-5525         TCGA-EJ-5526 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5527         TCGA-EJ-5530         TCGA-EJ-5531 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-5532         TCGA-EJ-5542         TCGA-EJ-7115 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7123         TCGA-EJ-7125         TCGA-EJ-7314 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7315         TCGA-EJ-7317         TCGA-EJ-7327 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7328         TCGA-EJ-7330         TCGA-EJ-7331 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7781         TCGA-EJ-7782         TCGA-EJ-7783 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7784         TCGA-EJ-7785         TCGA-EJ-7786 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7788         TCGA-EJ-7789         TCGA-EJ-7791 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EJ-7792         TCGA-EJ-7794         TCGA-FC-7708 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6329         TCGA-G9-6332         TCGA-G9-6333 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6336         TCGA-G9-6338         TCGA-G9-6342 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6343         TCGA-G9-6348         TCGA-G9-6351 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6353         TCGA-G9-6356         TCGA-G9-6361 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6362         TCGA-G9-6363         TCGA-G9-6364 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6365         TCGA-G9-6366         TCGA-G9-6367 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6369         TCGA-G9-6370         TCGA-G9-6371 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6373         TCGA-G9-6377         TCGA-G9-6378 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6384         TCGA-G9-6385         TCGA-G9-6494 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G9-6496         TCGA-G9-6499         TCGA-H9-7775 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HC-7230         TCGA-HC-7231         TCGA-HI-7168 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-HI-7169         TCGA-HI-7170         TCGA-HI-7171 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
[1] "hr=" "1"  
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      1    4
  22Q LOSS WILD-TYPE    4  114
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 1                  4
  YES                4                114
D20V4, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      0    5
  22Q LOSS WILD-TYPE    4  114
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 0                  4
  YES                5                114
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                   "NEOADJUVANT.THERAPY" 
> q(save="no")
