
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/146064/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC/1551578/1.GDAC_clinicalDataPicker.Finished/CESC.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC", "-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=CESC"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=31, in cluster file=68, common to both=14
[1] "Reduce the number of clustering variables from 78 to 20."
[1] 20 14
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 8 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 8 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                11 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                11 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                 6 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                 6 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                10 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                11 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                11 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 9 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 9 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 11 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                 8 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                 8 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                 8 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                 8 
[1] "5p loss mutation analysis"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                11 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                11 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                 7 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                 7 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                10 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 10 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                  9 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                  9 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                  8 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                  8 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  9 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  9 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 10 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  7 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  7 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  9 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  9 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 11 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 11 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "DAYSTODEATH"                           
 [3] "DAYSTOLASTFOLLOWUP"                    
 [4] "VITALSTATUS"                           
 [5] "DCCUPLOADDATE"                         
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "GENDER"                                
 [8] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
 [9] "HISTOLOGICALTYPE"                      
[10] "RADIATIONS.RADIATION.REGIMENINDICATION"
[11] "NEOADJUVANTTHERAPY"                    
[12] "BATCHNUMBER"                           

Input Data has 12 rows and 14 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
        1505          925         2155         1289           NA           81 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K 
        2127         2892            8           NA          178           37 
TCGA-FU-A23L TCGA-FU-A2QG 
          37           30 
Variable 1:'AGE':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=12,	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=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 14 columns, 1 survival variables, and 1 non-survival variables.
AGE, nv=12, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1q gain mutation analysis
D1V1, survival
                   sevent
clus2               0 1
  1Q GAIN MUTATED   6 0
  1Q GAIN WILD-TYPE 7 1
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                6                 8 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 1 
$`1Q GAIN MUTATED`
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EK-A2PI TCGA-FU-A23L 
       65.88        42.38        65.85        65.85        66.05         1.22 

$`1Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DS-A0VK TCGA-DS-A0VL TCGA-EA-A1QT TCGA-EX-A1H5 
       49.48        30.41        65.62         2.66         0.26         5.85 
TCGA-FU-A23K TCGA-FU-A2QG 
        1.22         0.99 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             1.22              0.26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            66.05             65.62 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           65.850             4.255 
[1] "1.2 - 66.0 (65.8)" "0.3 - 65.6 (4.3)" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
[1] "hr="     "2.8e+10"
D1V2, continuous

Clustering(2) Variable = 3p gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  0
  3P GAIN WILD-TYPE 10  1
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                11 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 1 
$`3P GAIN MUTATED`
TCGA-BI-A0VR TCGA-DS-A0VL TCGA-EA-A1QT 
       49.48         2.66         0.26 

$`3P GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN 
       30.41        65.88        42.38        65.62        65.85        65.85 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       66.05         5.85         1.22         1.22         0.99 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.26              0.99 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            49.48             66.05 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.66             42.38 
[1] "0.3 - 49.5 (2.7)"  "1.0 - 66.0 (42.4)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" NA   
D2V2, continuous

Clustering(3) Variable = 3q gain mutation analysis
D3V1, survival
                   sevent
clus2               0 1
  3Q GAIN MUTATED   7 1
  3Q GAIN WILD-TYPE 6 0
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                8                 6 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 0 
$`3Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT 
       49.48        30.41        65.62         2.66        65.85         0.26 
TCGA-EK-A2PI TCGA-FU-A23L 
       66.05         1.22 

$`3Q GAIN WILD-TYPE`
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
       65.88        42.38        65.85         5.85         1.22         0.99 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              0.99 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            66.05             65.88 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           39.945            24.115 
[1] "0.3 - 66.0 (39.9)" "1.0 - 65.9 (24.1)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
[1] "hr="     "1.1e+09"
D3V2, continuous

Clustering(4) Variable = 5p gain mutation analysis
D4V1, survival
                   sevent
clus2               0 1
  5P GAIN MUTATED   4 0
  5P GAIN WILD-TYPE 9 1
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                4                10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 1 
$`5P GAIN MUTATED`
TCGA-BI-A0VS TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23L 
       30.41        66.05         5.85         1.22 

$`5P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        65.88        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A23K TCGA-FU-A2QG 
       65.85         0.26         1.22         0.99 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.22              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            66.05             65.88 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.13             45.93 
[1] "1.2 - 66.0 (18.1)" "0.3 - 65.9 (45.9)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D4V2, continuous

Clustering(5) Variable = 6p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  0
  6P GAIN WILD-TYPE 10  1
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                11 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                0                 1 
$`6P GAIN MUTATED`
TCGA-BI-A0VS TCGA-FU-A23K TCGA-FU-A23L 
       30.41         1.22         1.22 

$`6P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        65.88        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A2QG 
       65.85         0.26        66.05         5.85         0.99 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.22              0.26 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            30.41             66.05 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.22             49.48 
[1] "1.2 - 30.4 (1.2)"  "0.3 - 66.0 (49.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
[1] "hr=" NA   
D5V2, continuous

Clustering(6) Variable = 8q gain mutation analysis
D6V1, survival
                   sevent
clus2               0 1
  8Q GAIN MUTATED   5 0
  8Q GAIN WILD-TYPE 8 1
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                 9 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 1 
$`8Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QT TCGA-FU-A23L 
       30.41         2.66        65.85         0.26         1.22 

$`8Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EK-A2PI 
       49.48        65.88        42.38        65.62        65.85        66.05 
TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
        5.85         1.22         0.99 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.26              0.99 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            65.85             66.05 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             2.66             49.48 
[1] "0.3 - 65.8 (2.7)"  "1.0 - 66.0 (49.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D6V2, continuous

Clustering(7) Variable = 20q gain mutation analysis
D7V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    3  0
  20Q GAIN WILD-TYPE 10  1
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 3                 11 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  1 
$`20Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-EA-A1QT TCGA-FU-A23K 
       30.41         0.26         1.22 

$`20Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        65.88        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG 
       65.85        66.05         5.85         1.22         0.99 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.99 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             30.41              66.05 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.22              49.48 
[1] "0.3 - 30.4 (1.2)"  "1.0 - 66.0 (49.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" NA   
D7V2, continuous

Clustering(8) Variable = 3p loss mutation analysis
D8V1, survival
                   sevent
clus2               0 1
  3P LOSS MUTATED   5 1
  3P LOSS WILD-TYPE 8 0
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                6                 8 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 0 
$`3P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EX-A1H5 TCGA-FU-A23L 
       65.88        65.62        65.85        65.85         5.85         1.22 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-EA-A1QT TCGA-EK-A2PI 
       49.48        30.41        42.38         2.66         0.26        66.05 
TCGA-FU-A23K TCGA-FU-A2QG 
        1.22         0.99 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             1.22              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            65.88             66.05 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           65.735            16.535 
[1] "1.2 - 65.9 (65.7)" "0.3 - 66.0 (16.5)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr="   "7e+08"
D8V2, continuous

Clustering(9) Variable = 4p loss mutation analysis
D9V1, survival
                   sevent
clus2               0 1
  4P LOSS MUTATED   5 1
  4P LOSS WILD-TYPE 8 0
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                6                 8 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                1                 0 
$`4P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EX-A1H5 TCGA-FU-A23L 
       65.88        65.62         2.66        65.85         5.85         1.22 

$`4P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-EA-A1QT TCGA-EK-A2PI 
       49.48        30.41        42.38        65.85         0.26        66.05 
TCGA-FU-A23K TCGA-FU-A2QG 
        1.22         0.99 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.22              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            65.88             66.05 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           35.735            36.395 
[1] "1.2 - 65.9 (35.7)" "0.3 - 66.0 (36.4)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "4P LOSS MUTATED"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D9V2, continuous

Clustering(10) Variable = 5p loss mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    2  1
  5P LOSS WILD-TYPE 11  0
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                3                11 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                1                 0 
$`5P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM 
       65.88        65.62        65.85 

$`5P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT 
       49.48        30.41        42.38         2.66        65.85         0.26 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       66.05         5.85         1.22         1.22         0.99 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            65.62              0.26 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            65.88             66.05 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            65.85              5.85 
[1] "65.6 - 65.9 (65.8)" "0.3 - 66.0 (5.8)"  
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5P LOSS MUTATED" "5P LOSS WILD-TYPE"   "5P LOSS MUTATED" "5P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"5P LOSS WILD-TYPE" "5P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D10V2, continuous

Clustering(11) Variable = 5q loss mutation analysis
D11V1, survival
                   sevent
clus2               0 1
  5Q LOSS MUTATED   6 1
  5Q LOSS WILD-TYPE 7 0
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                 7 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 0 
$`5Q LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-EA-A1QT TCGA-FU-A23L 
       65.88        65.62         2.66        65.85         0.26         1.22 
TCGA-FU-A2QG 
        0.99 

$`5Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-EK-A2PI TCGA-EX-A1H5 
       49.48        30.41        42.38        65.85        66.05         5.85 
TCGA-FU-A23K 
        1.22 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.26              1.22 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            65.88             66.05 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.66             42.38 
[1] "0.3 - 65.9 (2.7)"  "1.2 - 66.0 (42.4)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
  "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
[1] "hr="     "1.1e+09"
D11V2, continuous

Clustering(12) Variable = 8p loss mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    3  1
  8P LOSS WILD-TYPE 10  0
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                4                10 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 0 
$`8P LOSS MUTATED`
TCGA-DS-A0VK TCGA-EA-A1QT TCGA-EK-A2PI TCGA-FU-A23K 
       65.62         0.26        66.05         1.22 

$`8P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        65.88        42.38         2.66        65.85 
TCGA-DS-A0VN TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A2QG 
       65.85         5.85         1.22         0.99 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.99 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            66.05             65.88 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           33.420            36.395 
[1] "0.3 - 66.0 (33.4)" "1.0 - 65.9 (36.4)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-EA-A1QT        TCGA-EK-A2PI        TCGA-EX-A1H5        TCGA-FU-A23K 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+09"
D12V2, continuous

Clustering(13) Variable = 10p loss mutation analysis
D13V1, survival
                    sevent
clus2                0 1
  10P LOSS MUTATED   4 0
  10P LOSS WILD-TYPE 9 1
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 4                 10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  1 
$`10P LOSS MUTATED`
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
       66.05         5.85         1.22         0.99 

$`10P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       49.48        30.41        65.88        42.38        65.62         2.66 
TCGA-DS-A0VM TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A23L 
       65.85        65.85         0.26         1.22 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.99               0.26 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             66.05              65.88 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             3.535             45.930 
[1] "1.0 - 66.0 (3.5)"  "0.3 - 65.9 (45.9)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10P LOSS MUTATED"   "10P LOSS MUTATED"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
[1] "hr="   "7e+08"
D13V2, continuous

Clustering(14) Variable = 10q loss mutation analysis
D14V1, survival
                    sevent
clus2                0 1
  10Q LOSS MUTATED   4 1
  10Q LOSS WILD-TYPE 9 0
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                  9 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  0 
$`10Q LOSS MUTATED`
TCGA-DS-A0VK TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
       65.62        66.05         5.85         1.22         0.99 

$`10Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        65.88        42.38         2.66        65.85 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A23L 
       65.85         0.26         1.22 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.99               0.26 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             66.05              65.88 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              5.85              42.38 
[1] "1.0 - 66.0 (5.8)"  "0.3 - 65.9 (42.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "10Q LOSS MUTATED"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
[1] "hr="     "2.6e+09"
D14V2, continuous

Clustering(15) Variable = 11p loss mutation analysis
D15V1, survival
                    sevent
clus2                0 1
  11P LOSS MUTATED   5 1
  11P LOSS WILD-TYPE 8 0
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 6                  8 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  0 
$`11P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23L 
       65.88        65.62         0.26        66.05         5.85         1.22 

$`11P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        30.41        42.38         2.66        65.85        65.85 
TCGA-FU-A23K TCGA-FU-A2QG 
        1.22         0.99 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.26               0.99 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             66.05              65.85 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            35.735             36.395 
[1] "0.3 - 66.0 (35.7)" "1.0 - 65.8 (36.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11P LOSS MUTATED"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D15V2, continuous

Clustering(16) Variable = 11q loss mutation analysis
D16V1, survival
                    sevent
clus2                0 1
  11Q LOSS MUTATED   4 1
  11Q LOSS WILD-TYPE 9 0
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                  9 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  0 
$`11Q LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 
       65.88        65.62         0.26        66.05         5.85 

$`11Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        30.41        42.38         2.66        65.85        65.85 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        1.22         1.22         0.99 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.99 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             66.05              65.85 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             65.62              30.41 
[1] "0.3 - 66.0 (65.6)" "1.0 - 65.8 (30.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D16V2, continuous

Clustering(17) Variable = 12p loss mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    3  1
  12P LOSS WILD-TYPE 10  0
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 10 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  0 
$`12P LOSS MUTATED`
TCGA-DS-A0VK TCGA-DS-A0VL TCGA-EA-A1QT TCGA-FU-A2QG 
       65.62         2.66         0.26         0.99 

$`12P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        30.41        65.88        42.38        65.85        65.85 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L 
       66.05         5.85         1.22         1.22 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               1.22 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             65.62              66.05 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             1.825             45.930 
[1] "0.3 - 65.6 (1.8)"  "1.2 - 66.0 (45.9)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED"   "12P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
[1] "hr="     "2.8e+10"
D17V2, continuous

Clustering(18) Variable = 13q loss mutation analysis
D18V1, survival
                    sevent
clus2                0 1
  13Q LOSS MUTATED   7 0
  13Q LOSS WILD-TYPE 6 1
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 7                  7 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  1 
$`13Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 
       30.41        65.88        65.85         0.26        66.05         5.85 
TCGA-FU-A23L 
        1.22 

$`13Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-FU-A23K 
       49.48        42.38        65.62         2.66        65.85         1.22 
TCGA-FU-A2QG 
        0.99 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.26               0.99 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             66.05              65.85 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             30.41              42.38 
[1] "0.3 - 66.0 (30.4)" "1.0 - 65.8 (42.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+09"
D18V2, continuous

Clustering(19) Variable = 17p loss mutation analysis
D19V1, survival
                    sevent
clus2                0 1
  17P LOSS MUTATED   5 0
  17P LOSS WILD-TYPE 8 1
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 5                  9 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 0                  1 
$`17P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 
       65.88         2.66        65.85         0.26         5.85 

$`17P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-EK-A2PI 
       49.48        30.41        42.38        65.62        65.85        66.05 
TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        1.22         1.22         0.99 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.99 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             65.88              66.05 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              5.85              42.38 
[1] "0.3 - 65.9 (5.8)"  "1.0 - 66.0 (42.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D19V2, continuous

Clustering(20) Variable = 19p loss mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    3  0
  19P LOSS WILD-TYPE 10  1
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 11 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 0                  1 
$`19P LOSS MUTATED`
TCGA-DS-A0VM TCGA-EK-A2PI TCGA-FU-A23L 
       65.85        66.05         1.22 

$`19P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL 
       49.48        30.41        65.88        42.38        65.62         2.66 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG 
       65.85         0.26         5.85         1.22         0.99 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.22               0.26 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             66.05              65.88 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             65.85              30.41 
[1] "1.2 - 66.0 (65.8)" "0.3 - 65.9 (30.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EK-A2PI         TCGA-EX-A1H5         TCGA-FU-A23K 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG 
  "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D20V2, continuous
           V1.D              V2 
"Time to Death"           "AGE" 
> q(save="no")
