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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/285037/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/CESC-TP/2172423/1.GDAC_clinicalDataPicker.Finished/CESC-TP.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=CESC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=CESC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=32, in cluster file=102, common to both=26
[1] "Reduce the number of clustering variables from 80 to 35."
[1] 35 26
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                21 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                21 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                16 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                23 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                11 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                18 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                18 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                23 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                23 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                23 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                21 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                21 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 23 
[1] "12p gain mutation analysis"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 21 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 21 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 23 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 23 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 23 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 22 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 22 
[1] "16q gain mutation analysis"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 23 
[1] "18p gain mutation analysis"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 23 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 18 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 18 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 17 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 22 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 22 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                18 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                18 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                16 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                16 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                23 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                17 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                17 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                19 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                19 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 21 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 21 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 21 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 21 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 21 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 21 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 22 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 22 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 18 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 18 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 19 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 19 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 23 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 23 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 22 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 22 
[1] "20p loss mutation analysis"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 23 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 20 
[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] "NUMBERPACKYEARSSMOKED"                 
[12] "STOPPEDSMOKINGYEAR"                    
[13] "TOBACCOSMOKINGHISTORYINDICATOR"        
[14] "BATCHNUMBER"                           

Input Data has 14 rows and 26 columns.

[1] "Batch" "14"   
[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-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
        2127         2892          183            8           53           40 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
          25           19           NA          178          211           37 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI 
          37           30           66            2           31           44 
TCGA-HG-A2PA TCGA-HM-A3JK 
         773          168 
Variable 1:'AGE':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=24,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=9,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'NUMBERPACKYEARSSMOKED':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 12:'STOPPEDSMOKINGYEAR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 13:'TOBACCOSMOKINGHISTORYINDICATOR':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'BATCH.NUMBER':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                                   
[2] "RADIATIONS.RADIATION.REGIMENINDICATION"
[3] "NUMBERPACKYEARSSMOKED"                 
[4] "STOPPEDSMOKINGYEAR"                    
[5] "TOBACCOSMOKINGHISTORYINDICATOR"        
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 26 columns, 1 survival variables, and 5 non-survival variables.
AGE, nv=20, binary=FALSE, numeric=TRUE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=5, binary=FALSE, numeric=TRUE
STOPPEDSMOKINGYEAR, nv=4, binary=FALSE, numeric=TRUE
TOBACCOSMOKINGHISTORYINDICATOR, nv=4, binary=FALSE, numeric=TRUE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    5  0
  1P GAIN WILD-TYPE 20  1
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                5                21 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                0                 1 
$`1P GAIN MUTATED`
TCGA-DR-A0ZL TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-FU-A3NI TCGA-HM-A3JK 
       65.88         1.74         0.62         1.45         5.52 

$`1P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EK-A2PI 
       65.85         6.02         0.26         1.32         0.82        66.05 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.07         1.02        25.41 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.62              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            65.88             66.05 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.74              5.85 
[1] "0.6 - 65.9 (1.7)" "0.1 - 66.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
[1] "hr="   "7e+08"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      1    4
  1P GAIN WILD-TYPE    3   18
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                1                 3
  YES               4                18
D1V4, continuous
D1V5, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-DS-A3LQ        TCGA-FU-A2QG 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
D1V6, continuous

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   10  0
  1Q GAIN WILD-TYPE 15  1
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               10                16 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                0                 1 
$`1Q GAIN MUTATED`
TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EK-A2PI 
       65.88        42.38         6.02         1.74         0.62        66.05 
TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JK 
        1.22         2.17         1.45         5.52 

$`1Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        30.41        65.62         2.66        65.85        65.85 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K 
        0.26         1.32         0.82         5.85         6.94         1.22 
TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.99         0.07         1.02        25.41 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.62              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            66.05             65.85 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            3.845             4.255 
[1] "0.6 - 66.0 (3.8)" "0.1 - 65.8 (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 WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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 WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       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 WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
[1] "hr="     "1.1e+09"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2    8
  1Q GAIN WILD-TYPE    2   14
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 2
  YES               8                14
D2V4, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"       
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 4 
       TCGA-BI-A0VR        TCGA-EX-A1H5        TCGA-FU-A2QG        TCGA-FU-A3HY 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
D2V5, continuous
[1] "Remove cluster labels:" "1Q GAIN MUTATED"        "1Q GAIN WILD-TYPE"     
clus
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                2                 2 
named character(0)
D2V6, continuous

Clustering(3) Variable = 3p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    3  0
  3P GAIN WILD-TYPE 22  1
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                23 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                0                 1 
$`3P GAIN MUTATED`
TCGA-DS-A0VL TCGA-FU-A3NI TCGA-HM-A3JK 
        2.66         1.45         5.52 

$`3P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM 
       49.48        30.41        65.88        42.38        65.62        65.85 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
        0.62        66.05         5.85         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02        25.41 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.45              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             5.52             66.05 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             2.66              5.85 
[1] "1.4 - 5.5 (2.7)"  "0.1 - 66.0 (5.8)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"3P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
[1] "hr=" "1"  
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      1    2
  3P GAIN WILD-TYPE    3   20
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                1                 3
  YES               2                20
D3V4, continuous
D3V5, continuous
[1] "Remove cluster labels:" "3P GAIN MUTATED"       
clus
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-DS-A3LQ        TCGA-FU-A2QG 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
D3V6, continuous

Clustering(4) Variable = 3q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   14  1
  3Q GAIN WILD-TYPE 11  0
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               15                11 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                 0 
$`3Q GAIN MUTATED`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        65.88        65.62         2.66        65.85        65.85 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI 
        0.26         1.74         1.32         0.82         0.62        66.05 
TCGA-EX-A1H5 TCGA-FU-A3NI TCGA-HM-A3JK 
        5.85         1.45         5.52 

$`3Q GAIN WILD-TYPE`
TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A3LQ TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L 
       30.41        42.38         6.02         6.94         1.22         1.22 
TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        0.99         2.17         0.07         1.02        25.41 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.26              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            66.05             42.38 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             5.52              2.17 
[1] "0.3 - 66.0 (5.5)" "0.1 - 42.4 (2.2)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
  "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED"   "3Q GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
[1] "hr=" "1"  
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      3   12
  3Q GAIN WILD-TYPE    1   10
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                3                 1
  YES              12                10
D4V4, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"       
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 4 
       TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO        TCGA-FU-A3HY 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
D4V5, continuous
[1] "Remove cluster labels:" "3Q GAIN MUTATED"        "3Q GAIN WILD-TYPE"     
clus
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                2                 2 
named character(0)
D4V6, continuous

Clustering(5) Variable = 5p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    8  0
  5P GAIN WILD-TYPE 17  1
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                8                18 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                0                 1 
$`5P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A3LQ TCGA-EA-A3HR TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23L 
       30.41         6.02         1.32        66.05         5.85         1.22 
TCGA-FU-A3HY TCGA-FU-A3NI 
        0.07         1.45 

$`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-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 
       65.85         0.26         1.74         0.82         0.62         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.22         0.99         2.17         1.02        25.41         5.52 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.26 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            66.05             65.88 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             3.65              4.09 
[1] "0.1 - 66.0 (3.6)" "0.3 - 65.9 (4.1)"
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      2    6
  5P GAIN WILD-TYPE    2   16
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                2                 2
  YES               6                16
D5V4, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                2                 4 
       TCGA-BI-A0VR        TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D5V5, continuous
[1] "Remove cluster labels:" "5P GAIN MUTATED"       
clus
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-FU-A2QG        TCGA-HM-A3JK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
D5V6, continuous

Clustering(6) Variable = 6p gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    3  0
  6P GAIN WILD-TYPE 22  1
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                23 
  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-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62        66.05         5.85         6.94         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.22              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            30.41             66.05 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             1.22              5.52 
[1] "1.2 - 30.4 (1.2)" "0.1 - 66.0 (5.5)"
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0    3
  6P GAIN WILD-TYPE    4   19
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                0                 4
  YES               3                19
D6V4, continuous
D6V5, continuous
D6V6, continuous

Clustering(7) Variable = 8p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    3  0
  8P GAIN WILD-TYPE 22  1
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                23 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                0                 1 
$`8P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A3LQ TCGA-EA-A3HQ 
       30.41         6.02         1.74 

$`8P 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-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI 
       65.85         0.26         1.32         0.82         0.62        66.05 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             1.74              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            30.41             66.05 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             6.02              2.66 
[1] "1.7 - 30.4 (6.0)" "0.1 - 66.0 (2.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1    2
  8P GAIN WILD-TYPE    3   20
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 3
  YES               2                20
D7V4, continuous
D7V5, continuous
[1] "Remove cluster labels:" "8P GAIN MUTATED"       
clus
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-FU-A2QG        TCGA-HM-A3JK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
D7V6, continuous

Clustering(8) Variable = 8q gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED    5  0
  8Q GAIN WILD-TYPE 20  1
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                5                21 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                0                 1 
$`8Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-FU-A3NI 
       30.41        65.85         6.02         1.74         1.45 

$`8Q GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN 
       49.48        65.88        42.38        65.62         2.66        65.85 
TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 
        0.26         1.32         0.82         0.62        66.05         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             1.45              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            65.85             66.05 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             6.02              2.66 
[1] "1.4 - 65.8 (6.0)" "0.1 - 66.0 (2.7)"
       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 WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" "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 WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" "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 WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      1    4
  8Q GAIN WILD-TYPE    3   18
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                1                 3
  YES               4                18
D8V4, continuous
D8V5, continuous
[1] "Remove cluster labels:" "8Q GAIN MUTATED"       
clus
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-FU-A2QG        TCGA-HM-A3JK 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
D8V6, continuous

Clustering(9) Variable = 10p gain mutation analysis
D9V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    2  1
  10P GAIN WILD-TYPE 23  0
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 23 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 1                  0 
$`10P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A0VK TCGA-FU-A3NI 
       30.41        65.62         1.45 

$`10P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZL TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VM TCGA-DS-A0VN 
       49.48        65.88        42.38         2.66        65.85        65.85 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        6.02         0.26         1.74         1.32         0.82         0.62 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       66.05         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.45               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             65.62              66.05 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.41               2.66 
[1] "1.4 - 65.6 (30.4)" "0.1 - 66.0 (2.7)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr="     "2.8e+10"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0    3
  10P GAIN WILD-TYPE    4   19
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 0                  4
  YES                3                 19
D9V4, continuous
D9V5, continuous
D9V6, continuous

Clustering(10) Variable = 12p gain mutation analysis
D10V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED    5  0
  12P GAIN WILD-TYPE 20  1
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 5                 21 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 0                  1 
$`12P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3NI 
       30.41         6.02         1.22         2.17         1.45 

$`12P 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-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85         0.26         1.74         1.32         0.82         0.62 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3HY 
       66.05         5.85         6.94         1.22         0.99         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.22               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             30.41              66.05 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              2.17               5.52 
[1] "1.2 - 30.4 (2.2)" "0.1 - 66.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12P GAIN WILD-TYPE"   "12P GAIN MUTATED" "12P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12P GAIN MUTATED" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE"   "12P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
[1] "hr=" "1"  
D10V2, continuous
D10V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      1    4
  12P GAIN WILD-TYPE    3   18
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 1                  3
  YES                4                 18
D10V4, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D10V5, continuous
[1] "Remove cluster labels:" "12P GAIN MUTATED"      
clus
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" "12P GAIN WILD-TYPE" 
D10V6, continuous

Clustering(11) Variable = 12q gain mutation analysis
D11V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    3  0
  12Q GAIN WILD-TYPE 22  1
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 23 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                  1 
$`12Q GAIN MUTATED`
TCGA-DS-A3LQ TCGA-FU-A23L TCGA-FU-A3NI 
        6.02         1.22         1.45 

$`12Q GAIN 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-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85        65.85         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        0.62        66.05         5.85         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.22               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              6.02              66.05 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.45               5.52 
[1] "1.2 - 6.0 (1.4)"  "0.1 - 66.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1    2
  12Q GAIN WILD-TYPE    3   20
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  3
  YES                2                 20
D11V4, continuous
D11V5, continuous
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D11V6, continuous

Clustering(12) Variable = 15q gain mutation analysis
D12V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    3  0
  15Q GAIN WILD-TYPE 22  1
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 23 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 0                  1 
$`15Q GAIN MUTATED`
TCGA-EA-A3HQ TCGA-EX-A3L1 TCGA-FU-A23L 
        1.74         6.94         1.22 

$`15Q GAIN 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-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85        65.85         6.02         0.26         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62        66.05         5.85         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.22               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              6.94              66.05 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              1.74               5.52 
[1] "1.2 - 6.9 (1.7)"  "0.1 - 66.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1"  
D12V2, continuous
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    3
  15Q GAIN WILD-TYPE    4   19
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  4
  YES                3                 19
D12V4, continuous
D12V5, continuous
D12V6, continuous

Clustering(13) Variable = 16p gain mutation analysis
D13V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    4  0
  16P GAIN WILD-TYPE 21  1
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 22 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 0                  1 
$`16P GAIN MUTATED`
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EK-A2PI TCGA-FU-A3NI 
        6.02         1.74        66.05         1.45 

$`16P GAIN 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-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85        65.85         0.26         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02        25.41         5.52 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              1.45               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             66.05              65.88 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              3.88               4.09 
[1] "1.4 - 66.0 (3.9)" "0.1 - 65.9 (4.1)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE"   "16P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    3
  16P GAIN WILD-TYPE    3   19
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 1                  3
  YES                3                 19
D13V4, continuous
D13V5, continuous
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
D13V6, continuous

Clustering(14) Variable = 16q gain mutation analysis
D14V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED    3  0
  16Q GAIN WILD-TYPE 22  1
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 3                 23 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 0                  1 
$`16Q GAIN MUTATED`
TCGA-DS-A3LQ TCGA-EK-A2PI TCGA-EX-A3L1 
        6.02        66.05         6.94 

$`16Q GAIN 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-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85        65.85         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        0.62         5.85         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.02               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             66.05              65.88 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              6.94               2.17 
[1] "6.0 - 66.0 (6.9)" "0.1 - 65.9 (2.2)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"16Q GAIN WILD-TYPE"   "16Q GAIN MUTATED" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      1    2
  16Q GAIN WILD-TYPE    3   20
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 1                  3
  YES                2                 20
D14V4, continuous
D14V5, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
D14V6, continuous
[1] "Remove cluster labels:" "16Q GAIN MUTATED"      
clus
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-EA-A1QT 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-FU-A23K 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"16Q GAIN WILD-TYPE" "16Q GAIN WILD-TYPE" 

Clustering(15) Variable = 18p gain mutation analysis
D15V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED    3  0
  18P GAIN WILD-TYPE 22  1
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 3                 23 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 0                  1 
$`18P GAIN MUTATED`
TCGA-DR-A0ZL TCGA-DS-A3LQ TCGA-HM-A3JK 
       65.88         6.02         5.52 

$`18P GAIN WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85         0.26         1.74         1.32         0.82         0.62 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       66.05         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        2.17         0.07         1.02         1.45        25.41 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5.52               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             65.88              66.05 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              6.02               2.17 
[1] "5.5 - 65.9 (6.0)" "0.1 - 66.0 (2.2)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P GAIN WILD-TYPE"   "18P GAIN MUTATED" 
[1] "hr="   "7e+08"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      2    1
  18P GAIN WILD-TYPE    2   21
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 2                  2
  YES                1                 21
D15V4, continuous
D15V5, continuous
[1] "Remove cluster labels:" "18P GAIN MUTATED"       "18P GAIN WILD-TYPE"    
clus
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                  2 
named character(0)
D15V6, continuous

Clustering(16) Variable = 20p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    8  0
  20P GAIN WILD-TYPE 17  1
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 8                 18 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 0                  1 
$`20P GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-FU-A23K TCGA-FU-A3EO 
       30.41         6.02         1.74         0.82         1.22         2.17 
TCGA-FU-A3NI TCGA-HM-A3JK 
        1.45         5.52 

$`20P 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-EA-A3HR TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 
       65.85         0.26         1.32         0.62        66.05         5.85 
TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        6.94         1.22         0.99         0.07         1.02        25.41 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.82               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             30.41              66.05 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             1.955              6.395 
[1] "0.8 - 30.4 (2.0)" "0.1 - 66.0 (6.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
[1] "hr=" "1"  
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      2    6
  20P GAIN WILD-TYPE    2   16
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 2                  2
  YES                6                 16
D16V4, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"      
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
D16V5, continuous
[1] "Remove cluster labels:" "20P GAIN MUTATED"       "20P GAIN WILD-TYPE"    
clus
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 2                  2 
named character(0)
D16V6, continuous

Clustering(17) Variable = 20q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    9  0
  20Q GAIN WILD-TYPE 16  1
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 9                 17 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 0                  1 
$`20Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-FU-A23K 
       30.41         0.26         1.74         1.32         0.82         1.22 
TCGA-FU-A3EO TCGA-FU-A3NI TCGA-HM-A3JK 
        2.17         1.45         5.52 

$`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-DS-A3LQ TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 
       65.85         6.02         0.62        66.05         5.85         6.94 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.22         0.99         0.07         1.02        25.41 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             30.41              66.05 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              1.45               6.94 
[1] "0.3 - 30.4 (1.4)" "0.1 - 66.0 (6.9)"
        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-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        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-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        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-DS-A3LQ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20Q GAIN MUTATED"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
[1] "hr=" NA   
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      1    8
  20Q GAIN WILD-TYPE    3   14
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 1                  3
  YES                8                 14
D17V4, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
D17V5, continuous
[1] "Remove cluster labels:" "20Q GAIN MUTATED"      
clus
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-DS-A3LQ         TCGA-FU-A2QG 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
D17V6, continuous

Clustering(18) Variable = 22q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    4  0
  22Q GAIN WILD-TYPE 21  1
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 4                 22 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 0                  1 
$`22Q GAIN MUTATED`
TCGA-BI-A0VS TCGA-DS-A3LQ TCGA-EK-A2PI TCGA-FU-A3NI 
       30.41         6.02        66.05         1.45 

$`22Q 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-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85         0.26         1.74         1.32         0.82         0.62 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02        25.41         5.52 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.45               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             66.05              65.88 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            18.215              2.415 
[1] "1.4 - 66.0 (18.2)" "0.1 - 65.9 (2.4)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr="   "7e+08"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      1    3
  22Q GAIN WILD-TYPE    3   19
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 1                  3
  YES                3                 19
D18V4, continuous
D18V5, continuous
[1] "Remove cluster labels:" "22Q GAIN MUTATED"      
clus
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
D18V6, continuous

Clustering(19) Variable = 3p loss mutation analysis
D19V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    7  1
  3P LOSS WILD-TYPE 18  0
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                8                18 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                1                 0 
$`3P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VM TCGA-EA-A3HS TCGA-EX-A1H5 TCGA-FU-A23L 
       65.88        65.62        65.85         0.82         5.85         1.22 
TCGA-FU-A3HY TCGA-HG-A2PA 
        0.07        25.41 

$`3P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VL TCGA-DS-A0VN TCGA-DS-A3LQ 
       49.48        30.41        42.38         2.66        65.85         6.02 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A3L1 
        0.26         1.74         1.32         0.62        66.05         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HM-A3JK 
        1.22         0.99         2.17         1.02         1.45         5.52 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.07              0.26 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            65.88             66.05 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           15.630             2.415 
[1] "0.1 - 65.9 (15.6)" "0.3 - 66.0 (2.4)" 
       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 WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "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 WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "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 WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      1    7
  3P LOSS WILD-TYPE    3   15
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                1                 3
  YES               7                15
D19V4, continuous
[1] "Remove cluster labels:" "3P LOSS MUTATED"       
clus
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                 4 
       TCGA-BI-A0VR        TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
D19V5, continuous
D19V6, continuous

Clustering(20) Variable = 4p loss mutation analysis
D20V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    9  1
  4P LOSS WILD-TYPE 16  0
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                16 
  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-EA-A3HR TCGA-EA-A3HS 
       65.88        65.62         2.66        65.85         1.32         0.82 
TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3HY TCGA-FU-A3NI 
        5.85         1.22         0.07         1.45 

$`4P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A1QT 
       49.48        30.41        42.38        65.85         6.02         0.26 
TCGA-EA-A3HQ TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG 
        1.74         0.62        66.05         6.94         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         1.02        25.41         5.52 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.07              0.26 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            65.88             66.05 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            2.055             5.770 
[1] "0.1 - 65.9 (2.1)" "0.3 - 66.0 (5.8)"
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" "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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      2    8
  4P LOSS WILD-TYPE    2   14
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                2                 2
  YES               8                14
D20V4, continuous
[1] "Remove cluster labels:" "4P LOSS MUTATED"       
clus
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                2                 4 
       TCGA-BI-A0VR        TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
D20V5, continuous
D20V6, continuous

Clustering(21) Variable = 4q loss mutation analysis
D21V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    3  0
  4Q LOSS WILD-TYPE 22  1
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                3                23 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                0                 1 
$`4Q LOSS MUTATED`
TCGA-DR-A0ZL TCGA-EX-A1H5 TCGA-FU-A3NI 
       65.88         5.85         1.45 

$`4Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        42.38        65.62         2.66        65.85 
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62        66.05         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         0.07         1.02        25.41         5.52 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             1.45              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            65.88             66.05 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             5.85              2.66 
[1] "1.4 - 65.9 (5.8)" "0.1 - 66.0 (2.7)"
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BI-A0VR        TCGA-BI-A0VS        TCGA-DR-A0ZL        TCGA-DR-A0ZM 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A0VK        TCGA-DS-A0VL        TCGA-DS-A0VM        TCGA-DS-A0VN 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr="   "7e+08"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      1    2
  4Q LOSS WILD-TYPE    3   20
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                1                 3
  YES               2                20
D21V4, continuous
[1] "Remove cluster labels:" "4Q LOSS MUTATED"       
clus
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                1                 5 
       TCGA-BI-A0VR        TCGA-DR-A0ZM        TCGA-FU-A2QG        TCGA-FU-A3EO 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FU-A3HY 
"4Q LOSS WILD-TYPE" 
D21V5, continuous
D21V6, continuous

Clustering(22) Variable = 5q loss mutation analysis
D22V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    8  1
  5Q LOSS WILD-TYPE 17  0
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9                17 
  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 TCGA-FU-A3HY TCGA-HG-A2PA 
        0.99         0.07        25.41 

$`5Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A3HQ 
       49.48        30.41        42.38        65.85         6.02         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 
        1.32         0.82         0.62        66.05         5.85         6.94 
TCGA-FU-A23K TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HM-A3JK 
        1.22         2.17         1.02         1.45         5.52 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.07              0.62 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            65.88             66.05 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.66              5.52 
[1] "0.1 - 65.9 (2.7)" "0.6 - 66.0 (5.5)"
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       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-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED"   "5Q LOSS MUTATED" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
  "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      0    9
  5Q LOSS WILD-TYPE    4   13
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                0                 4
  YES               9                13
D22V4, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                2                 4 
       TCGA-BI-A0VR        TCGA-DR-A0ZM        TCGA-EX-A1H5        TCGA-FU-A3EO 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D22V5, continuous
[1] "Remove cluster labels:" "5Q LOSS MUTATED"       
clus
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                1                 3 
       TCGA-BI-A0VR        TCGA-DS-A3LQ        TCGA-HM-A3JK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
D22V6, continuous

Clustering(23) Variable = 8p loss mutation analysis
D23V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED    6  1
  8P LOSS WILD-TYPE 19  0
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                7                19 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
                1                 0 
$`8P LOSS MUTATED`
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EA-A3HR TCGA-EK-A2PI TCGA-FU-A23K 
       65.62        65.85         0.26         1.32        66.05         1.22 
TCGA-FU-A3NI 
        1.45 

$`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-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 
        6.02         1.74         0.82         0.62         5.85         6.94 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.22         0.99         2.17         0.07         1.02        25.41 
TCGA-HM-A3JK 
        5.52 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.26              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            66.05             65.88 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             1.45              5.52 
[1] "0.3 - 66.0 (1.4)" "0.1 - 65.9 (5.5)"
       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 MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"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 MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"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 MUTATED" 
       TCGA-DS-A3LQ        TCGA-EA-A1QT        TCGA-EA-A3HQ        TCGA-EA-A3HR 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EA-A3HS        TCGA-EA-A3HT        TCGA-EK-A2PI        TCGA-EX-A1H5 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EX-A3L1        TCGA-FU-A23K        TCGA-FU-A23L        TCGA-FU-A2QG 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FU-A3EO        TCGA-FU-A3HY        TCGA-FU-A3HZ        TCGA-FU-A3NI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-HG-A2PA        TCGA-HM-A3JK 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      1    6
  8P LOSS WILD-TYPE    3   16
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                1                 3
  YES               6                16
D23V4, continuous
D23V5, continuous
D23V6, continuous

Clustering(24) Variable = 10p loss mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    5  0
  10P LOSS WILD-TYPE 20  1
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 5                 21 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 0                  1 
$`10P LOSS MUTATED`
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-HM-A3JK 
       66.05         5.85         1.22         0.99         5.52 

$`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-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR 
       65.85        65.85         6.02         0.26         1.74         1.32 
TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.82         0.62         6.94         1.22         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        1.02         1.45        25.41 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.99               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             66.05              65.88 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              5.52               2.66 
[1] "1.0 - 66.0 (5.5)" "0.1 - 65.9 (2.7)"
        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-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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-DS-A3LQ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" 
[1] "hr="   "7e+08"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      2    3
  10P LOSS WILD-TYPE    2   19
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 2                  2
  YES                3                 19
D24V4, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  4 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A3EO 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FU-A3HY 
"10P LOSS WILD-TYPE" 
D24V5, continuous
[1] "Remove cluster labels:" "10P LOSS MUTATED"       "10P LOSS WILD-TYPE"    
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                  2 
named character(0)
D24V6, continuous

Clustering(25) Variable = 10q loss mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    4  1
  10Q LOSS WILD-TYPE 21  0
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 1                  0 
$`10Q LOSS MUTATED`
TCGA-DS-A0VK TCGA-EX-A1H5 TCGA-FU-A23K TCGA-FU-A2QG TCGA-HM-A3JK 
       65.62         5.85         1.22         0.99         5.52 

$`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-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85         6.02         0.26         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A3L1 TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        0.62        66.05         6.94         1.22         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA 
        1.02         1.45        25.41 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.99               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             65.62              66.05 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              5.52               2.66 
[1] "1.0 - 65.6 (5.5)" "0.1 - 66.0 (2.7)"
        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-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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-DS-A3LQ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
[1] "hr="     "2.8e+10"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      2    3
  10Q LOSS WILD-TYPE    2   19
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 2                  2
  YES                3                 19
D25V4, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"      
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  4 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A3EO 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY 
"10Q LOSS WILD-TYPE" 
D25V5, continuous
[1] "Remove cluster labels:" "10Q LOSS MUTATED"       "10Q LOSS WILD-TYPE"    
clus
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 2                  2 
named character(0)
D25V6, continuous

Clustering(26) Variable = 11p loss mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    5  0
  11P LOSS WILD-TYPE 20  1
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 21 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 0                  1 
$`11P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EX-A1H5 TCGA-FU-A23L TCGA-FU-A3NI 
       65.88        65.85         5.85         1.22         1.45 

$`11P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        42.38        65.62         2.66        65.85 
TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
        6.02         0.26         1.74         1.32         0.82         0.62 
TCGA-EK-A2PI TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
       66.05         6.94         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              1.22               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             65.88              66.05 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.85               2.66 
[1] "1.2 - 65.9 (5.8)" "0.1 - 66.0 (2.7)"
        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 WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "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 WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "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 WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2    3
  11P LOSS WILD-TYPE    2   19
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 2                  2
  YES                3                 19
D26V4, continuous
[1] "Remove cluster labels:" "11P LOSS MUTATED"      
clus
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A2QG 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
D26V5, continuous
D26V6, continuous

Clustering(27) Variable = 11q loss mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    5  0
  11Q LOSS WILD-TYPE 20  1
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 5                 21 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 0                  1 
$`11Q LOSS MUTATED`
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A3NI 
       65.85         0.26        66.05         5.85         1.45 

$`11Q 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-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85         6.02         1.74         1.32         0.82         0.62 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY 
        6.94         1.22         1.22         0.99         2.17         0.07 
TCGA-FU-A3HZ TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02        25.41         5.52 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.26               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             66.05              65.88 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              5.85               2.66 
[1] "0.3 - 66.0 (5.8)" "0.1 - 65.9 (2.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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 WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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 WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      2    3
  11Q LOSS WILD-TYPE    2   19
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 2                  2
  YES                3                 19
D27V4, continuous
[1] "Remove cluster labels:" "11Q LOSS MUTATED"      
clus
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A2QG 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
D27V5, continuous
D27V6, continuous

Clustering(28) Variable = 12p loss mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    3  1
  12P LOSS WILD-TYPE 22  0
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 22 
  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-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI 
        6.02         1.74         1.32         0.82         0.62        66.05 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A3EO TCGA-FU-A3HY 
        5.85         6.94         1.22         1.22         2.17         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02         1.45        25.41         5.52 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.26               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             65.62              66.05 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             1.825              5.685 
[1] "0.3 - 65.6 (1.8)" "0.1 - 66.0 (5.7)"
        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-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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-DS-A3LQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr="     "2.8e+10"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    4
  12P LOSS WILD-TYPE    4   18
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 0                  4
  YES                4                 18
D28V4, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D28V5, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-DS-A3LQ         TCGA-HM-A3JK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D28V6, continuous

Clustering(29) Variable = 13q loss mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED    8  0
  13Q LOSS WILD-TYPE 17  1
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                 18 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 0                  1 
$`13Q LOSS MUTATED`
TCGA-DS-A0VN TCGA-DS-A3LQ TCGA-EA-A1QT TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-FU-A23L 
       65.85         6.02         0.26        66.05         5.85         1.22 
TCGA-FU-A3NI TCGA-HG-A2PA 
        1.45        25.41 

$`13Q 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-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EX-A3L1 
       65.85         1.74         1.32         0.82         0.62         6.94 
TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HM-A3JK 
        1.22         0.99         2.17         0.07         1.02         5.52 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.26               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             66.05              65.88 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             5.935              2.415 
[1] "0.3 - 66.0 (5.9)" "0.1 - 65.9 (2.4)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        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-DS-A3LQ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        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-DS-A3LQ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        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-DS-A3LQ 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      3    5
  13Q LOSS WILD-TYPE    1   17
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 3                  1
  YES                5                 17
D29V4, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A2QG 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D29V5, continuous
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                  3 
        TCGA-BI-A0VR         TCGA-FU-A2QG         TCGA-HM-A3JK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
D29V6, continuous

Clustering(30) Variable = 17p loss mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED    6  1
  17P LOSS WILD-TYPE 19  0
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 7                 19 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  0 
$`17P LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-EX-A1H5 
       65.88        65.62         2.66        65.85         0.26         5.85 
TCGA-FU-A3NI 
        1.45 

$`17P LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VM TCGA-DS-A3LQ TCGA-EA-A3HQ 
       49.48        30.41        42.38        65.85         6.02         1.74 
TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A3L1 TCGA-FU-A23K 
        1.32         0.82         0.62        66.05         6.94         1.22 
TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-HG-A2PA 
        1.22         0.99         2.17         0.07         1.02        25.41 
TCGA-HM-A3JK 
        5.52 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.26               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             65.88              66.05 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              5.85               2.17 
[1] "0.3 - 65.9 (5.8)" "0.1 - 66.0 (2.2)"
        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 MUTATED"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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 MUTATED"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"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 MUTATED"   "17P LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      2    5
  17P LOSS WILD-TYPE    2   17
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 2                  2
  YES                5                 17
D30V4, continuous
[1] "Remove cluster labels:" "17P LOSS MUTATED"      
clus
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-FU-A2QG 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HY 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
D30V5, continuous
D30V6, continuous

Clustering(31) Variable = 17q loss mutation analysis
D31V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    2  1
  17Q LOSS WILD-TYPE 23  0
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 23 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 1                  0 
$`17Q LOSS MUTATED`
TCGA-DS-A0VK TCGA-DS-A0VN TCGA-EA-A1QT 
       65.62        65.85         0.26 

$`17Q 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-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI 
        6.02         1.74         1.32         0.82         0.62        66.05 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3EO 
        5.85         6.94         1.22         1.22         0.99         2.17 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.26               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             65.85              66.05 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             65.62               2.66 
[1] "0.3 - 65.8 (65.6)" "0.1 - 66.0 (2.7)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"17Q LOSS WILD-TYPE"   "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "17Q LOSS MUTATED" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+09"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      1    2
  17Q LOSS WILD-TYPE    3   20
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 1                  3
  YES                2                 20
D31V4, continuous
D31V5, continuous
D31V6, continuous

Clustering(32) Variable = 18p loss mutation analysis
D32V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  0
  18P LOSS WILD-TYPE 22  1
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 3                 23 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 0                  1 
$`18P LOSS MUTATED`
TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A3EO 
       65.85         0.26         2.17 

$`18P 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-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT 
       65.85         6.02         1.74         1.32         0.82         0.62 
TCGA-EK-A2PI TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
       66.05         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3HY TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        0.07         1.02         1.45        25.41         5.52 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.26               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             65.85              66.05 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              2.17               5.52 
[1] "0.3 - 65.8 (2.2)" "0.1 - 66.0 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr="   "7e+08"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      1    2
  18P LOSS WILD-TYPE    3   20
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 1                  3
  YES                2                 20
D32V4, continuous
[1] "Remove cluster labels:" "18P LOSS MUTATED"      
clus
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
D32V5, continuous
D32V6, continuous

Clustering(33) Variable = 18q loss mutation analysis
D33V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    4  0
  18Q LOSS WILD-TYPE 21  1
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 22 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 0                  1 
$`18Q LOSS MUTATED`
TCGA-DR-A0ZL TCGA-DS-A0VN TCGA-EA-A1QT TCGA-FU-A3EO 
       65.88        65.85         0.26         2.17 

$`18Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-BI-A0VS TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VL TCGA-DS-A0VM 
       49.48        30.41        42.38        65.62         2.66        65.85 
TCGA-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI 
        6.02         1.74         1.32         0.82         0.62        66.05 
TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG TCGA-FU-A3HY 
        5.85         6.94         1.22         1.22         0.99         0.07 
TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        1.02         1.45        25.41         5.52 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.26               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             65.88              66.05 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             34.01               4.09 
[1] "0.3 - 65.9 (34.0)" "0.1 - 66.0 (4.1)" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr="     "1.1e+09"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      1    3
  18Q LOSS WILD-TYPE    3   19
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 1                  3
  YES                3                 19
D33V4, continuous
[1] "Remove cluster labels:" "18Q LOSS MUTATED"      
clus
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3HY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
D33V5, continuous
D33V6, continuous

Clustering(34) Variable = 20p loss mutation analysis
D34V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED    3  0
  20P LOSS WILD-TYPE 22  1
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 3                 23 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 0                  1 
$`20P LOSS MUTATED`
TCGA-EA-A1QT TCGA-EK-A2PI TCGA-FU-A3HY 
        0.26        66.05         0.07 

$`20P 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-DS-A3LQ TCGA-EA-A3HQ TCGA-EA-A3HR TCGA-EA-A3HS 
       65.85        65.85         6.02         1.74         1.32         0.82 
TCGA-EA-A3HT TCGA-EX-A1H5 TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A23L TCGA-FU-A2QG 
        0.62         5.85         6.94         1.22         1.22         0.99 
TCGA-FU-A3EO TCGA-FU-A3HZ TCGA-FU-A3NI TCGA-HG-A2PA TCGA-HM-A3JK 
        2.17         1.02         1.45        25.41         5.52 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.07               0.62 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             66.05              65.88 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.26               5.52 
[1] "0.1 - 66.0 (0.3)" "0.6 - 65.9 (5.5)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE"   "20P LOSS MUTATED" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
  "20P LOSS MUTATED" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
[1] "hr="   "7e+08"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0    3
  20P LOSS WILD-TYPE    4   19
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  4
  YES                3                 19
D34V4, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                  5 
        TCGA-BI-A0VR         TCGA-DR-A0ZM         TCGA-EX-A1H5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A2QG         TCGA-FU-A3EO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D34V5, continuous
D34V6, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 2                 23 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HQ         TCGA-EA-A3HR         TCGA-EA-A3HS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EA-A3HT         TCGA-EX-A1H5         TCGA-EX-A3L1 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A23K         TCGA-FU-A23L         TCGA-FU-A2QG 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-FU-A3EO         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 

Clustering(35) Variable = 21q loss mutation analysis
D35V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    6  0
  21Q LOSS WILD-TYPE 19  1
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 20 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 0                  1 
$`21Q LOSS MUTATED`
TCGA-BI-A0VS TCGA-DR-A0ZL TCGA-DS-A0VL TCGA-EA-A3HR TCGA-FU-A23L TCGA-FU-A3NI 
       30.41        65.88         2.66         1.32         1.22         1.45 

$`21Q LOSS WILD-TYPE`
TCGA-BI-A0VR TCGA-DR-A0ZM TCGA-DS-A0VK TCGA-DS-A0VM TCGA-DS-A0VN TCGA-DS-A3LQ 
       49.48        42.38        65.62        65.85        65.85         6.02 
TCGA-EA-A1QT TCGA-EA-A3HQ TCGA-EA-A3HS TCGA-EA-A3HT TCGA-EK-A2PI TCGA-EX-A1H5 
        0.26         1.74         0.82         0.62        66.05         5.85 
TCGA-EX-A3L1 TCGA-FU-A23K TCGA-FU-A2QG TCGA-FU-A3EO TCGA-FU-A3HY TCGA-FU-A3HZ 
        6.94         1.22         0.99         2.17         0.07         1.02 
TCGA-HG-A2PA TCGA-HM-A3JK 
       25.41         5.52 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.22               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             65.88              66.05 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             2.055              5.685 
[1] "1.2 - 65.9 (2.1)" "0.1 - 66.0 (5.7)"
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BI-A0VR         TCGA-BI-A0VS         TCGA-DR-A0ZL 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED"   "21Q LOSS MUTATED" 
        TCGA-DR-A0ZM         TCGA-DS-A0VK         TCGA-DS-A0VL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-DS-A0VM         TCGA-DS-A0VN         TCGA-DS-A3LQ 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EA-A1QT         TCGA-EA-A3HQ         TCGA-EA-A3HR 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-EA-A3HS         TCGA-EA-A3HT         TCGA-EK-A2PI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EX-A1H5         TCGA-EX-A3L1         TCGA-FU-A23K 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A23L         TCGA-FU-A2QG         TCGA-FU-A3EO 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FU-A3HY         TCGA-FU-A3HZ         TCGA-FU-A3NI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-HG-A2PA         TCGA-HM-A3JK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr="   "7e+08"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    6
  21Q LOSS WILD-TYPE    4   16
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 0                  4
  YES                6                 16
D35V4, continuous
D35V5, continuous
D35V6, continuous
                                    V1.D 
                         "Time to Death" 
                                      V2 
                                   "AGE" 
                                      V3 
"RADIATIONS.RADIATION.REGIMENINDICATION" 
                                      V4 
                 "NUMBERPACKYEARSSMOKED" 
                                      V5 
                    "STOPPEDSMOKINGYEAR" 
                                      V6 
        "TOBACCOSMOKINGHISTORYINDICATOR" 
> q(save="no")
