
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/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/SARC-TP/3472563/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SARC-TP/3353001/SARC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=SARC-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=SARC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=29, in cluster file=52, common to both=22
[1] "Reduce the number of clustering variables from 80 to 47."
[1] 47 22
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3                19 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3                19 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                3                19 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                3                19 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
                5                17 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                5                17 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                4                18 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                4                18 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                17 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                17 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                6                16 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                6                16 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
                7                15 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                7                15 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                7                15 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                7                15 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                18 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                18 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                4                18 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                4                18 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                19 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                19 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 4                 18 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 4                 18 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 19 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 19 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                 16 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                 16 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 3                 19 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 3                 19 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 18 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 18 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 5                 17 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 5                 17 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                 16 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                 16 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 4                 18 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 4                 18 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 7                 15 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 7                 15 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 9                 13 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 9                 13 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                 17 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                 17 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                 19 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                 19 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
                3                19 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                3                19 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4                18 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4                18 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                19 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                19 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                3                19 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                3                19 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                18 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                18 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                5                17 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                5                17 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
                3                19 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                3                19 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                3                19 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                3                19 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
                6                16 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                6                16 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                18 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                18 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 9                 13 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 9                 13 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 9                 13 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 9                 13 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 8                 14 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 8                 14 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 6                 16 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 6                 16 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 13 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 13 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 5                 17 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 5                 17 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                 19 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                 19 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 4                 18 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 4                 18 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 8                 14 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 8                 14 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 18 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 18 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 5                 17 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 5                 17 
[1] "19q loss"
[1] 3
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                 19 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                 19 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 4                 18 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 4                 18 
[1] "Xq loss"
[1] 3
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                4                18 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                4                18 
[1] "data2feature, selection="
[1] "YEARSTOBIRTH"                          
[2] "DAYSTODEATH"                           
[3] "DAYSTOLASTFOLLOWUP"                    
[4] "VITALSTATUS"                           
[5] "DCCUPLOADDATE"                         
[6] "GENDER"                                
[7] "RADIATIONTHERAPY"                      
[8] "RADIATIONS.RADIATION.REGIMENINDICATION"
[9] "BATCHNUMBER"                           

Input Data has 9 rows and 22 columns.

[1] "Batch" "9"    
[1] "Last Follow UP"
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
          62          827           NA          745           NA         1420 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
        1291          960          260           NA         1620         1309 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
          14            3            2            2          818           NA 
TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
         126           NA           NA          181 
Variable 1:'AGE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'BATCH.NUMBER':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 22 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=14, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN CNV        3  0
  1P GAIN WILD-TYPE 13  6
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3                19 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                0                 6 
$`1P GAIN CNV`
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-KF-A41W 
       26.89         4.14         5.95 

$`1P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       42.44        31.56         8.55         9.70        53.26        43.04 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-IS-A3KA 
        0.46         0.10         0.07         0.07         4.54        13.58 
TCGA-IW-A3M5 
        5.88 

      1P GAIN CNV 1P GAIN WILD-TYPE 
             4.14              0.07 
      1P GAIN CNV 1P GAIN WILD-TYPE 
            26.89             53.26 
      1P GAIN CNV 1P GAIN WILD-TYPE 
             5.95             12.85 
[1] "4.1 - 26.9 (6.0)"  "0.1 - 53.3 (12.8)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "1P GAIN CNV" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "1P GAIN CNV" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "1P GAIN CNV" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "1P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P GAIN WILD-TYPE"       "1P GAIN CNV" 
[1] "hr="     "2.2e+08"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    0
  1P GAIN WILD-TYPE    7   12
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  FEMALE           3                 7
  MALE             0                12

Clustering(2) Variable = 4p gain
D2V1, survival
                   sevent
clus2                0  1
  4P GAIN CNV        1  2
  4P GAIN WILD-TYPE 15  4
      4P GAIN CNV 4P GAIN WILD-TYPE 
                3                19 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                2                 4 
$`4P GAIN CNV`
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-HB-A3YV 
       18.51        46.68         4.54 

$`4P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.07         0.07        26.89         4.14        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             4.54              0.07 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            46.68             53.26 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            18.51              9.70 
[1] "4.5 - 46.7 (18.5)" "0.1 - 53.3 (9.7)" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "4P GAIN CNV"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          0    3
  4P GAIN WILD-TYPE   10    9
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           0                10
  MALE             3                 9

Clustering(3) Variable = 5p gain
D3V1, survival
                   sevent
clus2                0  1
  5P GAIN CNV        3  2
  5P GAIN WILD-TYPE 13  4
      5P GAIN CNV 5P GAIN WILD-TYPE 
                5                17 
      5P GAIN CNV 5P GAIN WILD-TYPE 
                2                 4 
$`5P GAIN CNV`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IW-A3M5 
       27.19        46.68        26.89         4.54         5.88 

$`5P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        12.85        24.49        18.51        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        0.07         0.07         4.14        13.58         5.95 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             4.54              0.07 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            46.68             53.26 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            26.89              9.70 
[1] "4.5 - 46.7 (26.9)" "0.1 - 53.3 (9.7)" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5P GAIN CNV" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          3    2
  5P GAIN WILD-TYPE    7   10
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  FEMALE           3                 7
  MALE             2                10

Clustering(4) Variable = 5q gain
D4V1, survival
                   sevent
clus2                0  1
  5Q GAIN CNV        1  3
  5Q GAIN WILD-TYPE 15  3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                4                18 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                3                 3 
$`5Q GAIN CNV`
TCGA-DX-A1L1 TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 
       46.68         4.54        13.58         5.88 

$`5Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
        2.04        27.19        12.85        24.49        18.51        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       31.56         8.55         9.70        53.26        43.04         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-KF-A41W 
        0.10         0.07         0.07        26.89         4.14         5.95 

      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             4.54              0.07 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            46.68             53.26 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            9.730            11.275 
[1] "4.5 - 46.7 (9.7)"  "0.1 - 53.3 (11.3)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
[1] "hr=" "4.5"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          2    2
  5Q GAIN WILD-TYPE    8   10
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  FEMALE           2                 8
  MALE             2                10

Clustering(5) Variable = 6p gain
D5V1, survival
                   sevent
clus2                0  1
  6P GAIN CNV        3  2
  6P GAIN WILD-TYPE 13  4
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                17 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                2                 4 
$`6P GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A2J1 TCGA-HB-A3YV TCGA-IW-A3M5 
        2.04        27.19        53.26         4.54         5.88 

$`6P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        24.49        18.51        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55         9.70        43.04         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        0.07        26.89         4.14        13.58         5.95 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             2.04              0.07 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            53.26             46.68 
      6P GAIN CNV 6P GAIN WILD-TYPE 
             5.88             12.85 
[1] "2.0 - 53.3 (5.9)"  "0.1 - 46.7 (12.8)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6P GAIN CNV" "6P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          2    3
  6P GAIN WILD-TYPE    8    9
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  FEMALE           2                 8
  MALE             3                 9

Clustering(6) Variable = 6q gain
D6V1, survival
                   sevent
clus2                0  1
  6Q GAIN CNV        3  3
  6Q GAIN WILD-TYPE 13  3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                6                16 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                 3 
$`6Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A2J1 TCGA-HB-A3YV TCGA-IW-A3M5 
        2.04        27.19        18.51        53.26         4.54         5.88 

$`6Q GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ 
       12.85        24.49        46.68        42.44        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
        9.70        43.04         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
       26.89         4.14        13.58         5.95 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             2.04              0.07 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            53.26             46.68 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
           12.195            11.275 
[1] "2.0 - 53.3 (12.2)" "0.1 - 46.7 (11.3)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          2    4
  6Q GAIN WILD-TYPE    8    8
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  FEMALE           2                 8
  MALE             4                 8

Clustering(7) Variable = 7p gain
D7V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV        4  3
  7P GAIN WILD-TYPE 12  3
      7P GAIN CNV 7P GAIN WILD-TYPE 
                7                15 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                3                 3 
$`7P GAIN CNV`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
       27.19        12.85        42.44         0.07        26.89         4.54 
TCGA-IS-A3KA 
       13.58 

$`7P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ 
        2.04        24.49        18.51        46.68        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G 
        9.70        53.26        43.04         0.46         0.10         0.07 
TCGA-HB-A43Z TCGA-IW-A3M5 TCGA-KF-A41W 
        4.14         5.88         5.95 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             0.07              0.07 
      7P GAIN CNV 7P GAIN WILD-TYPE 
            42.44             53.26 
      7P GAIN CNV 7P GAIN WILD-TYPE 
            13.58              8.55 
[1] "0.1 - 42.4 (13.6)" "0.1 - 53.3 (8.6)" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7P GAIN CNV"       "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          4    3
  7P GAIN WILD-TYPE    6    9
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE           4                 6
  MALE             3                 9

Clustering(8) Variable = 7q gain
D8V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV        4  3
  7Q GAIN WILD-TYPE 12  3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                7                15 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                3                 3 
$`7Q GAIN CNV`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV 
       27.19        12.85        42.44         0.07        26.89         4.54 
TCGA-IS-A3KA 
       13.58 

$`7Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ 
        2.04        24.49        18.51        46.68        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G 
        9.70        53.26        43.04         0.46         0.10         0.07 
TCGA-HB-A43Z TCGA-IW-A3M5 TCGA-KF-A41W 
        4.14         5.88         5.95 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             0.07              0.07 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            42.44             53.26 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            13.58              8.55 
[1] "0.1 - 42.4 (13.6)" "0.1 - 53.3 (8.6)" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
      "7Q GAIN CNV"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          4    3
  7Q GAIN WILD-TYPE    6    9
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE           4                 6
  MALE             3                 9

Clustering(9) Variable = 8p gain
D9V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV        1  3
  8P GAIN WILD-TYPE 15  3
      8P GAIN CNV 8P GAIN WILD-TYPE 
                4                18 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                3                 3 
$`8P GAIN CNV`
TCGA-DX-A1KY TCGA-FX-A3NJ TCGA-IS-A3KA TCGA-IW-A3M5 
       12.85         0.10        13.58         5.88 

$`8P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       31.56         8.55         9.70        53.26        43.04         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-KF-A41W 
        0.07         0.07        26.89         4.54         4.14         5.95 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             0.10              0.07 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            13.58             53.26 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            9.365            14.105 
[1] "0.1 - 13.6 (9.4)"  "0.1 - 53.3 (14.1)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" 
[1] "hr=" "7.7"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          2    2
  8P GAIN WILD-TYPE    8   10
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE           2                 8
  MALE             2                10

Clustering(10) Variable = 8q gain
D10V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV        2  2
  8Q GAIN WILD-TYPE 14  4
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                4                18 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
                2                 4 
$`8Q GAIN CNV`
TCGA-DX-A1KY TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-IW-A3M5 
       12.85         0.46         0.10         5.88 

$`8Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3RE 
       31.56         8.55         9.70        53.26        43.04         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        0.07        26.89         4.54         4.14        13.58         5.95 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             0.10              0.07 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            12.85             53.26 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            3.170            16.045 
[1] "0.1 - 12.8 (3.2)"  "0.1 - 53.3 (16.0)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
[1] "hr=" "8.4"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV          2    2
  8Q GAIN WILD-TYPE    8   10
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE           2                 8
  MALE             2                10

Clustering(11) Variable = 9q gain
D11V1, survival
                   sevent
clus2                0  1
  9Q GAIN CNV        3  0
  9Q GAIN WILD-TYPE 13  6
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                19 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                0                 6 
$`9Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-FX-A2QS 
        2.04        24.49         0.46 

$`9Q GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       27.19        12.85        18.51        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55         9.70        53.26        43.04         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.07        26.89         4.54         4.14        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             0.46              0.07 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
            24.49             53.26 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             2.04             12.85 
[1] "0.5 - 24.5 (2.0)"  "0.1 - 53.3 (12.8)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          1    2
  9Q GAIN WILD-TYPE    9   10
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  FEMALE           1                 9
  MALE             2                10

Clustering(12) Variable = 15q gain
D12V1, survival
                    sevent
clus2                 0  1
  15Q GAIN CNV        3  1
  15Q GAIN WILD-TYPE 13  5
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 4                 18 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 1                  5 
$`15Q GAIN CNV`
TCGA-DX-A1KX TCGA-DX-A2IZ TCGA-HB-A43Z TCGA-IS-A3KA 
       27.19         8.55         4.14        13.58 

$`15Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        12.85        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
       31.56         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07         0.07        26.89         4.54         5.88         5.95 

      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              4.14               0.07 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             27.19              53.26 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
            11.065             11.275 
[1] "4.1 - 27.2 (11.1)" "0.1 - 53.3 (11.3)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "15Q GAIN CNV"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"15Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "15Q GAIN CNV"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"15Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "15Q GAIN CNV"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"15Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          3    1
  15Q GAIN WILD-TYPE    7   11
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  FEMALE            3                  7
  MALE              1                 11

Clustering(13) Variable = 16p gain
D13V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV        2  1
  16P GAIN WILD-TYPE 14  5
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 19 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 1                  5 
$`16P GAIN CNV`
TCGA-DX-A1KW TCGA-FX-A2QS TCGA-IS-A3KA 
        2.04         0.46        13.58 

$`16P GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ 
       31.56         8.55         9.70        53.26        43.04         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IW-A3M5 
        0.07         0.07        26.89         4.54         4.14         5.88 
TCGA-KF-A41W 
        5.95 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              0.46               0.07 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             13.58              53.26 
      16P GAIN CNV 16P GAIN WILD-TYPE 
              2.04              12.85 
[1] "0.5 - 13.6 (2.0)"  "0.1 - 53.3 (12.8)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"16P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"16P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "16P GAIN CNV" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"16P GAIN WILD-TYPE"       "16P GAIN CNV" "16P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"16P GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          2    1
  16P GAIN WILD-TYPE    8   11
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE            2                  8
  MALE              1                 11

Clustering(14) Variable = 17p gain
D14V1, survival
                    sevent
clus2                 0  1
  17P GAIN CNV        4  2
  17P GAIN WILD-TYPE 12  4
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 6                 16 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                  4 
$`17P GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-FX-A3RE TCGA-HB-A3YV 
        2.04        12.85        46.68        42.44         0.07         4.54 

$`17P GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 
       27.19        24.49        18.51        31.56         8.55         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT 
       53.26        43.04         0.46         0.10         0.07        26.89 
TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        4.14        13.58         5.88         5.95 

      17P GAIN CNV 17P GAIN WILD-TYPE 
              0.07               0.07 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             46.68              53.26 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             8.695             11.640 
[1] "0.1 - 46.7 (8.7)"  "0.1 - 53.3 (11.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17P GAIN CNV" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          1    5
  17P GAIN WILD-TYPE    9    7
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  FEMALE            1                  9
  MALE              5                  7

Clustering(15) Variable = 17q gain
D15V1, survival
                    sevent
clus2                 0  1
  17Q GAIN CNV        3  0
  17Q GAIN WILD-TYPE 13  6
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 3                 19 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 0                  6 
$`17Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-FX-A3RE 
        2.04        42.44         0.07 

$`17Q GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       27.19        12.85        24.49        18.51        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.07        26.89         4.54         4.14        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              0.07               0.07 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             42.44              53.26 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              2.04              12.85 
[1] "0.1 - 42.4 (2.0)"  "0.1 - 53.3 (12.8)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"17Q GAIN WILD-TYPE" 
[1] "hr="     "7.6e+07"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          1    2
  17Q GAIN WILD-TYPE    9   10
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  FEMALE            1                  9
  MALE              2                 10

Clustering(16) Variable = 18p gain
D16V1, survival
                    sevent
clus2                 0  1
  18P GAIN CNV        3  1
  18P GAIN WILD-TYPE 13  5
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 4                 18 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                  5 
$`18P GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-HB-A43Z TCGA-IS-A3KA 
        2.04        31.56         4.14        13.58 

$`18P GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       27.19        12.85        24.49        18.51        46.68        42.44 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07         0.07        26.89         4.54         5.88         5.95 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              2.04               0.07 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             31.56              53.26 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             8.860             11.275 
[1] "2.0 - 31.6 (8.9)"  "0.1 - 53.3 (11.3)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P GAIN WILD-TYPE"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          3    1
  18P GAIN WILD-TYPE    7   11
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            3                  7
  MALE              1                 11

Clustering(17) Variable = 18q gain
D17V1, survival
                    sevent
clus2                 0  1
  18Q GAIN CNV        4  1
  18Q GAIN WILD-TYPE 12  5
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 5                 17 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                  5 
$`18Q GAIN CNV`
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-FX-A2QS TCGA-HB-A43Z TCGA-IS-A3KA 
       42.44        31.56         0.46         4.14        13.58 

$`18Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55         9.70        53.26        43.04         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07        26.89         4.54         5.88         5.95 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              0.46               0.07 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             42.44              53.26 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             13.58               9.70 
[1] "0.5 - 42.4 (13.6)" "0.1 - 53.3 (9.7)" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "18Q GAIN CNV"       "18Q GAIN CNV" "18Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"18Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          4    1
  18Q GAIN WILD-TYPE    6   11
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            4                  6
  MALE              1                 11

Clustering(18) Variable = 19p gain
D18V1, survival
                    sevent
clus2                 0  1
  19P GAIN CNV        4  2
  19P GAIN WILD-TYPE 12  4
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 6                 16 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 2                  4 
$`19P GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-FX-A3RE TCGA-IW-A3M5 
        2.04        27.19        12.85        46.68         0.07         5.88 

$`19P GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 
       24.49        18.51        42.44        31.56         8.55         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT 
       53.26        43.04         0.46         0.10         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        4.54         4.14        13.58         5.95 

      19P GAIN CNV 19P GAIN WILD-TYPE 
              0.07               0.07 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             46.68              53.26 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             9.365             11.640 
[1] "0.1 - 46.7 (9.4)"  "0.1 - 53.3 (11.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19P GAIN CNV"       "19P GAIN CNV"       "19P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KF-A41W 
"19P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19P GAIN CNV"       "19P GAIN CNV"       "19P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KF-A41W 
"19P GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19P GAIN CNV"       "19P GAIN CNV"       "19P GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-KF-A41W 
"19P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          3    3
  19P GAIN WILD-TYPE    7    9
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  FEMALE            3                  7
  MALE              3                  9

Clustering(19) Variable = 19q gain
D19V1, survival
                    sevent
clus2                 0  1
  19Q GAIN CNV        3  1
  19Q GAIN WILD-TYPE 13  5
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 4                 18 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 1                  5 
$`19Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 
        2.04        27.19        12.85        46.68 

$`19Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 
       24.49        18.51        42.44        31.56         8.55         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       53.26        43.04         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
       26.89         4.54         4.14        13.58         5.88         5.95 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              2.04               0.07 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             46.68              53.26 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
            20.020              9.125 
[1] "2.0 - 46.7 (20.0)" "0.1 - 53.3 (9.1)" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"19Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"19Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "19Q GAIN CNV"       "19Q GAIN CNV"       "19Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"19Q GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          1    3
  19Q GAIN WILD-TYPE    9    9
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  FEMALE            1                  9
  MALE              3                  9

Clustering(20) Variable = 20p gain
D20V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV        4  3
  20P GAIN WILD-TYPE 12  3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 7                 15 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 3                  3 
$`20P GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-IS-A3KA TCGA-IW-A3M5 
        2.04        27.19        18.51        46.68        13.58         5.88 
TCGA-KF-A41W 
        5.95 

$`20P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 
       12.85        24.49        42.44        31.56         8.55         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       53.26        43.04         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       26.89         4.54         4.14 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              2.04               0.07 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             46.68              53.26 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             13.58               9.70 
[1] "2.0 - 46.7 (13.6)" "0.1 - 53.3 (9.7)" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-KF-A41W 
      "20P GAIN CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-KF-A41W 
      "20P GAIN CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20P GAIN CNV"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20P GAIN WILD-TYPE"       "20P GAIN CNV"       "20P GAIN CNV" 
        TCGA-KF-A41W 
      "20P GAIN CNV" 
[1] "hr=" "1.7"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          4    3
  20P GAIN WILD-TYPE    6    9
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE            4                  6
  MALE              3                  9

Clustering(21) Variable = 20q gain
D21V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV        4  5
  20Q GAIN WILD-TYPE 12  1
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 9                 13 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 5                  1 
$`20Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-HB-A3YV 
        2.04        27.19        12.85        18.51        46.68         4.54 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
       13.58         5.88         5.95 

$`20Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       24.49        42.44        31.56         8.55         9.70        53.26 
TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       43.04         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z 
        4.14 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              2.04               0.07 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             46.68              53.26 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             12.85               9.70 
[1] "2.0 - 46.7 (12.8)" "0.1 - 53.3 (9.7)" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-KF-A41W 
      "20Q GAIN CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-KF-A41W 
      "20Q GAIN CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "20Q GAIN CNV"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV"       "20Q GAIN CNV" 
        TCGA-KF-A41W 
      "20Q GAIN CNV" 
[1] "hr=" "6.8"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          4    5
  20Q GAIN WILD-TYPE    6    7
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE            4                  6
  MALE              5                  7

Clustering(22) Variable = 21q gain
D22V1, survival
                    sevent
clus2                 0  1
  21Q GAIN CNV        3  2
  21Q GAIN WILD-TYPE 13  4
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 5                 17 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 2                  4 
$`21Q GAIN CNV`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A2IZ TCGA-HB-A3YV 
        2.04        12.85        46.68         8.55         4.54 

$`21Q GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2J0 
       27.19        24.49        18.51        42.44        31.56         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       53.26        43.04         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
       26.89         4.14        13.58         5.88         5.95 

      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              2.04               0.07 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
             46.68              53.26 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              8.55              13.58 
[1] "2.0 - 46.7 (8.6)"  "0.1 - 53.3 (13.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"21Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"21Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"       "21Q GAIN CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"21Q GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          0    5
  21Q GAIN WILD-TYPE   10    7
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  FEMALE            0                 10
  MALE              5                  7

Clustering(23) Variable = 22q gain
D23V1, survival
                    sevent
clus2                 0  1
  22Q GAIN CNV        2  1
  22Q GAIN WILD-TYPE 14  5
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 3                 19 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 1                  5 
$`22Q GAIN CNV`
TCGA-DX-A1KY TCGA-HB-A2OT TCGA-HB-A43Z 
       12.85        26.89         4.14 

$`22Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       31.56         8.55         9.70        53.26        43.04         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 
        0.10         0.07         0.07         4.54        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              4.14               0.07 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             26.89              53.26 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             12.85               9.70 
[1] "4.1 - 26.9 (12.8)" "0.1 - 53.3 (9.7)" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"22Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"22Q GAIN WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-KF-A41W 
"22Q GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          2    1
  22Q GAIN WILD-TYPE    8   11
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  FEMALE            2                  8
  MALE              1                 11

Clustering(24) Variable = 1p loss
D24V1, survival
                   sevent
clus2                0  1
  1P LOSS CNV        2  1
  1P LOSS WILD-TYPE 14  5
      1P LOSS CNV 1P LOSS WILD-TYPE 
                3                19 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                1                 5 
$`1P LOSS CNV`
TCGA-DX-A1L0 TCGA-FX-A3RE TCGA-FX-A48G 
       18.51         0.07         0.07 

$`1P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        12.85        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       31.56         8.55         9.70        53.26        43.04         0.46 
TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.10        26.89         4.54         4.14        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.07              0.10 
      1P LOSS CNV 1P LOSS WILD-TYPE 
            18.51             53.26 
      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.07             12.85 
[1] "0.1 - 18.5 (0.1)"  "0.1 - 53.3 (12.8)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "2.1"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          2    1
  1P LOSS WILD-TYPE    8   11
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           2                 8
  MALE             1                11

Clustering(25) Variable = 1q loss
D25V1, survival
                   sevent
clus2                0  1
  1Q LOSS CNV        2  2
  1Q LOSS WILD-TYPE 14  4
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                4                18 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                2                 4 
$`1Q LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-FX-A48G 
       18.51        42.44         9.70         0.07 

$`1Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55        53.26        43.04         0.46         0.10         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
       26.89         4.54         4.14        13.58         5.88         5.95 

      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             0.07              0.07 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
            42.44             53.26 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
           14.105            10.700 
[1] "0.1 - 42.4 (14.1)" "0.1 - 53.3 (10.7)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          1    3
  1Q LOSS WILD-TYPE    9    9
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  FEMALE           1                 9
  MALE             3                 9

Clustering(26) Variable = 2p loss
D26V1, survival
                   sevent
clus2                0  1
  2P LOSS CNV        1  2
  2P LOSS WILD-TYPE 15  4
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                19 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                 4 
$`2P LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-IS-A3KA 
       18.51        42.44        13.58 

$`2P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IW-A3M5 
        0.07         0.07        26.89         4.54         4.14         5.88 
TCGA-KF-A41W 
        5.95 

      2P LOSS CNV 2P LOSS WILD-TYPE 
            13.58              0.07 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            42.44             53.26 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            18.51              8.55 
[1] "13.6 - 42.4 (18.5)" "0.1 - 53.3 (8.6)"  
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2P LOSS CNV" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          1    2
  2P LOSS WILD-TYPE    9   10
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  FEMALE           1                 9
  MALE             2                10

Clustering(27) Variable = 2q loss
D27V1, survival
                   sevent
clus2                0  1
  2Q LOSS CNV        1  2
  2Q LOSS WILD-TYPE 15  4
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                3                19 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2                 4 
$`2Q LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-IS-A3KA 
       18.51        42.44        13.58 

$`2Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IW-A3M5 
        0.07         0.07        26.89         4.54         4.14         5.88 
TCGA-KF-A41W 
        5.95 

      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            13.58              0.07 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            42.44             53.26 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            18.51              8.55 
[1] "13.6 - 42.4 (18.5)" "0.1 - 53.3 (8.6)"  
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "2Q LOSS CNV" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          1    2
  2Q LOSS WILD-TYPE    9   10
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  FEMALE           1                 9
  MALE             2                10

Clustering(28) Variable = 3p loss
D28V1, survival
                   sevent
clus2                0  1
  3P LOSS CNV        2  2
  3P LOSS WILD-TYPE 14  4
      3P LOSS CNV 3P LOSS WILD-TYPE 
                4                18 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                 4 
$`3P LOSS CNV`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-HB-A3YV TCGA-HB-A43Z 
       27.19        18.51         4.54         4.14 

$`3P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07         0.07        26.89        13.58         5.88         5.95 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             4.14              0.07 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            27.19             53.26 
      3P LOSS CNV 3P LOSS WILD-TYPE 
           11.525            11.275 
[1] "4.1 - 27.2 (11.5)" "0.1 - 53.3 (11.3)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3P LOSS CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          2    2
  3P LOSS WILD-TYPE    8   10
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           2                 8
  MALE             2                10

Clustering(29) Variable = 3q loss
D29V1, survival
                   sevent
clus2                0  1
  3Q LOSS CNV        3  2
  3Q LOSS WILD-TYPE 13  4
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                5                17 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                 4 
$`3Q LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-HB-A3YV TCGA-HB-A43Z 
        2.04        27.19        18.51         4.54         4.14 

$`3Q LOSS WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ 
       12.85        24.49        46.68        42.44        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        9.70        53.26        43.04         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07        26.89        13.58         5.88         5.95 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             2.04              0.07 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            27.19             53.26 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             4.54             12.85 
[1] "2.0 - 27.2 (4.5)"  "0.1 - 53.3 (12.8)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "3Q LOSS CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"3Q LOSS WILD-TYPE"       "3Q LOSS CNV"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          2    3
  3Q LOSS WILD-TYPE    8    9
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           2                 8
  MALE             3                 9

Clustering(30) Variable = 4p loss
D30V1, survival
                   sevent
clus2                0  1
  4P LOSS CNV        2  1
  4P LOSS WILD-TYPE 14  5
      4P LOSS CNV 4P LOSS WILD-TYPE 
                3                19 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                1                 5 
$`4P LOSS CNV`
TCGA-DX-A2IZ TCGA-HB-A43Z TCGA-IW-A3M5 
        8.55         4.14         5.88 

$`4P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       42.44        31.56         9.70        53.26        43.04         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IS-A3KA 
        0.10         0.07         0.07        26.89         4.54        13.58 
TCGA-KF-A41W 
        5.95 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             4.14              0.07 
      4P LOSS CNV 4P LOSS WILD-TYPE 
             8.55             53.26 
      4P LOSS CNV 4P LOSS WILD-TYPE 
             5.88             13.58 
[1] "4.1 - 8.6 (5.9)"   "0.1 - 53.3 (13.6)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" 
[1] "hr=" "6.7"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          2    1
  4P LOSS WILD-TYPE    8   11
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  FEMALE           2                 8
  MALE             1                11

Clustering(31) Variable = 4q loss
D31V1, survival
                   sevent
clus2                0  1
  4Q LOSS CNV        2  1
  4Q LOSS WILD-TYPE 14  5
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                3                19 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                1                 5 
$`4Q LOSS CNV`
TCGA-DX-A2IZ TCGA-HB-A43Z TCGA-IW-A3M5 
        8.55         4.14         5.88 

$`4Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS 
       42.44        31.56         9.70        53.26        43.04         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IS-A3KA 
        0.10         0.07         0.07        26.89         4.54        13.58 
TCGA-KF-A41W 
        5.95 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             4.14              0.07 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             8.55             53.26 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             5.88             13.58 
[1] "4.1 - 8.6 (5.9)"   "0.1 - 53.3 (13.6)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
[1] "hr=" "6.7"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          2    1
  4Q LOSS WILD-TYPE    8   11
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  FEMALE           2                 8
  MALE             1                11

Clustering(32) Variable = 8p loss
D32V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV        6  0
  8P LOSS WILD-TYPE 10  6
      8P LOSS CNV 8P LOSS WILD-TYPE 
                6                16 
      8P LOSS CNV 8P LOSS WILD-TYPE 
                0                 6 
$`8P LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A43Z 
        2.04        24.49        42.44         0.46         0.07         4.14 

$`8P LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ 
       27.19        12.85        18.51        46.68        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT 
        9.70        53.26        43.04         0.10         0.07        26.89 
TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        4.54        13.58         5.88         5.95 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             0.07              0.07 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            42.44             53.26 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            3.090            13.215 
[1] "0.1 - 42.4 (3.1)"  "0.1 - 53.3 (13.2)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV          3    3
  8P LOSS WILD-TYPE    7    9
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE           3                 7
  MALE             3                 9

Clustering(33) Variable = 9p loss
D33V1, survival
                   sevent
clus2                0  1
  9P LOSS CNV        2  2
  9P LOSS WILD-TYPE 14  4
      9P LOSS CNV 9P LOSS WILD-TYPE 
                4                18 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                2                 4 
$`9P LOSS CNV`
TCGA-DX-A1KY TCGA-FX-A2QS TCGA-FX-A3RE TCGA-IW-A3M5 
       12.85         0.46         0.07         5.88 

$`9P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        24.49        18.51        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ 
       31.56         8.55         9.70        53.26        43.04         0.10 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        0.07        26.89         4.54         4.14        13.58         5.95 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             0.07              0.07 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            12.85             53.26 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            3.170            16.045 
[1] "0.1 - 12.8 (3.2)"  "0.1 - 53.3 (16.0)"
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" 
[1] "hr=" "8.4"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          3    1
  9P LOSS WILD-TYPE    7   11
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  FEMALE           3                 7
  MALE             1                11

Clustering(34) Variable = 10p loss
D34V1, survival
                    sevent
clus2                0 1
  10P LOSS CNV       7 2
  10P LOSS WILD-TYPE 9 4
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 9                 13 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                  4 
$`10P LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
        2.04        18.51         0.46         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-IW-A3M5 TCGA-KF-A41W 
        4.14         5.88         5.95 

$`10P LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       27.19        12.85        24.49        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-HB-A3YV 
        8.55         9.70        53.26        43.04         0.10         4.54 
TCGA-IS-A3KA 
       13.58 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              0.07               0.10 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             26.89              53.26 
      10P LOSS CNV 10P LOSS WILD-TYPE 
              4.14              24.49 
[1] "0.1 - 26.9 (4.1)"  "0.1 - 53.3 (24.5)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KF-A41W 
      "10P LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KF-A41W 
      "10P LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "10P LOSS CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10P LOSS CNV"       "10P LOSS CNV" "10P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10P LOSS CNV" "10P LOSS WILD-TYPE"       "10P LOSS CNV" 
        TCGA-KF-A41W 
      "10P LOSS CNV" 
[1] "hr=" "1.8"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          7    2
  10P LOSS WILD-TYPE    3   10
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            7                  3
  MALE              2                 10

Clustering(35) Variable = 10q loss
D35V1, survival
                    sevent
clus2                0 1
  10Q LOSS CNV       7 2
  10Q LOSS WILD-TYPE 9 4
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 9                 13 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 2                  4 
$`10Q LOSS CNV`
TCGA-DX-A1L0 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       18.51         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        4.14        13.58         5.95 

$`10Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        12.85        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-HB-A3YV 
       31.56         8.55         9.70        53.26        43.04         4.54 
TCGA-IW-A3M5 
        5.88 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              0.07               2.04 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             26.89              53.26 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              4.14              24.49 
[1] "0.1 - 26.9 (4.1)"  "2.0 - 53.3 (24.5)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10Q LOSS CNV"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "10Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10Q LOSS CNV"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "10Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "10Q LOSS CNV"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "10Q LOSS CNV"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "10Q LOSS CNV" 
[1] "hr=" "1.4"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          7    2
  10Q LOSS WILD-TYPE    3   10
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            7                  3
  MALE              2                 10

Clustering(36) Variable = 11p loss
D36V1, survival
                    sevent
clus2                 0  1
  11P LOSS CNV        5  3
  11P LOSS WILD-TYPE 11  3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 8                 14 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 3                  3 
$`11P LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-FX-A3RE 
        2.04        24.49        18.51        42.44         9.70         0.07 
TCGA-HB-A43Z TCGA-IW-A3M5 
        4.14         5.88 

$`11P LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J1 
       27.19        12.85        46.68        31.56         8.55        53.26 
TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV 
       43.04         0.46         0.10         0.07        26.89         4.54 
TCGA-IS-A3KA TCGA-KF-A41W 
       13.58         5.95 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.07               0.07 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             42.44              53.26 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             7.790             13.215 
[1] "0.1 - 42.4 (7.8)"  "0.1 - 53.3 (13.2)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-KF-A41W 
"11P LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-KF-A41W 
"11P LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11P LOSS CNV"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11P LOSS CNV" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "11P LOSS CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        TCGA-KF-A41W 
"11P LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          3    5
  11P LOSS WILD-TYPE    7    7
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  FEMALE            3                  7
  MALE              5                  7

Clustering(37) Variable = 11q loss
D37V1, survival
                    sevent
clus2                 0  1
  11Q LOSS CNV        3  3
  11Q LOSS WILD-TYPE 13  3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 6                 16 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 3                  3 
$`11Q LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-IW-A3M5 
        2.04        24.49        18.51        42.44         9.70         5.88 

$`11Q LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J1 
       27.19        12.85        46.68        31.56         8.55        53.26 
TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT 
       43.04         0.46         0.10         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        4.54         4.14        13.58         5.95 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              2.04               0.07 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             42.44              53.26 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
            14.105             10.700 
[1] "2.0 - 42.4 (14.1)" "0.1 - 53.3 (10.7)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-KF-A41W 
"11Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-KF-A41W 
"11Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "11Q LOSS CNV"       "11Q LOSS CNV" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        TCGA-KF-A41W 
"11Q LOSS WILD-TYPE" 
[1] "hr=" "2.2"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          1    5
  11Q LOSS WILD-TYPE    9    7
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  FEMALE            1                  9
  MALE              5                  7

Clustering(38) Variable = 13q loss
D38V1, survival
                    sevent
clus2                 0  1
  13Q LOSS CNV        6  3
  13Q LOSS WILD-TYPE 10  3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 9                 13 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 3                  3 
$`13Q LOSS CNV`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A2J0 TCGA-FX-A3RE TCGA-FX-A48G 
       27.19        18.51        46.68         9.70         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-KF-A41W 
        4.54         4.14         5.95 

$`13Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ 
        2.04        12.85        24.49        42.44        31.56         8.55 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-HB-A2OT TCGA-IS-A3KA 
       53.26        43.04         0.46         0.10        26.89        13.58 
TCGA-IW-A3M5 
        5.88 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              0.07               0.10 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             46.68              53.26 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              5.95              13.58 
[1] "0.1 - 46.7 (6.0)"  "0.1 - 53.3 (13.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "13Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "13Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "13Q LOSS CNV" 
[1] "hr=" "2.1"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          5    4
  13Q LOSS WILD-TYPE    5    8
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            5                  5
  MALE              4                  8

Clustering(39) Variable = 14q loss
D39V1, survival
                    sevent
clus2                 0  1
  14Q LOSS CNV        5  0
  14Q LOSS WILD-TYPE 11  6
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 5                 17 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 0                  6 
$`14Q LOSS CNV`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-FX-A2QS TCGA-FX-A48G 
        2.04        24.49        42.44         0.46         0.07 

$`14Q LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A2IZ 
       27.19        12.85        18.51        46.68        31.56         8.55 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT 
        9.70        53.26        43.04         0.10         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        4.54         4.14        13.58         5.88         5.95 

      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              0.07               0.07 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             42.44              53.26 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              2.04              12.85 
[1] "0.1 - 42.4 (2.0)"  "0.1 - 53.3 (12.8)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"14Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"14Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"14Q LOSS WILD-TYPE" 
[1] "hr="     "2.5e+08"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          2    3
  14Q LOSS WILD-TYPE    8    9
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  FEMALE            2                  8
  MALE              3                  9

Clustering(40) Variable = 15q loss
D40V1, survival
                    sevent
clus2                 0  1
  15Q LOSS CNV        1  2
  15Q LOSS WILD-TYPE 15  4
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                 19 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 2                  4 
$`15Q LOSS CNV`
TCGA-FX-A48G TCGA-HB-A3YV TCGA-IW-A3M5 
        0.07         4.54         5.88 

$`15Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       42.44        31.56         8.55         9.70        53.26        43.04 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3KA 
        0.46         0.10         0.07        26.89         4.14        13.58 
TCGA-KF-A41W 
        5.95 

      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              0.07               0.07 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              5.88              53.26 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              4.54              13.58 
[1] "0.1 - 5.9 (4.5)"   "0.1 - 53.3 (13.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-KF-A41W 
"15Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-KF-A41W 
"15Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-KF-A41W 
"15Q LOSS WILD-TYPE" 
[1] "hr="     "6.1e+09"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          2    1
  15Q LOSS WILD-TYPE    8   11
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  FEMALE            2                  8
  MALE              1                 11

Clustering(41) Variable = 16p loss
D41V1, survival
                    sevent
clus2                 0  1
  16P LOSS CNV        3  1
  16P LOSS WILD-TYPE 13  5
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 4                 18 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 1                  5 
$`16P LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-FX-A48G TCGA-HB-A43Z 
       18.51        42.44         0.07         4.14 

$`16P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
        8.55         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
        0.07        26.89         4.54        13.58         5.88         5.95 

      16P LOSS CNV 16P LOSS WILD-TYPE 
              0.07               0.07 
      16P LOSS CNV 16P LOSS WILD-TYPE 
             42.44              53.26 
      16P LOSS CNV 16P LOSS WILD-TYPE 
            11.325             11.275 
[1] "0.1 - 42.4 (11.3)" "0.1 - 53.3 (11.3)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16P LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16P LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D41V2, continuous
D41V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          2    2
  16P LOSS WILD-TYPE    8   10
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  FEMALE            2                  8
  MALE              2                 10

Clustering(42) Variable = 16q loss
D42V1, survival
                    sevent
clus2                 0  1
  16Q LOSS CNV        5  3
  16Q LOSS WILD-TYPE 11  3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 8                 14 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 3                  3 
$`16Q LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       18.51        42.44         9.70         0.10         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z 
        4.54         4.14 

$`16Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        27.19        12.85        24.49        46.68        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-HB-A2OT TCGA-IS-A3KA 
        8.55        53.26        43.04         0.46        26.89        13.58 
TCGA-IW-A3M5 TCGA-KF-A41W 
        5.88         5.95 

      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              0.07               0.46 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             42.44              53.26 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             4.340             19.035 
[1] "0.1 - 42.4 (4.3)"  "0.5 - 53.3 (19.0)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"16Q LOSS WILD-TYPE" 
[1] "hr=" "3.6"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          3    5
  16Q LOSS WILD-TYPE    7    7
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  FEMALE            3                  7
  MALE              5                  7

Clustering(43) Variable = 18p loss
D43V1, survival
                    sevent
clus2                 0  1
  18P LOSS CNV        1  3
  18P LOSS WILD-TYPE 15  3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 18 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 3                  3 
$`18P LOSS CNV`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-KF-A41W 
       12.85        18.51         9.70         5.95 

$`18P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        27.19        24.49        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55        53.26        43.04         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.07        26.89         4.54         4.14        13.58         5.88 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              5.95               0.07 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             18.51              53.26 
      18P LOSS CNV 18P LOSS WILD-TYPE 
            11.275             11.065 
[1] "6.0 - 18.5 (11.3)" "0.1 - 53.3 (11.1)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18P LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18P LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18P LOSS CNV" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18P LOSS CNV" 
[1] "hr=" "4.5"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          1    3
  18P LOSS WILD-TYPE    9    9
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  FEMALE            1                  9
  MALE              3                  9

Clustering(44) Variable = 18q loss
D44V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV        2  3
  18Q LOSS WILD-TYPE 14  3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 5                 17 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 3                  3 
$`18Q LOSS CNV`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-FX-A48G TCGA-KF-A41W 
       12.85        18.51         9.70         0.07         5.95 

$`18Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        27.19        24.49        46.68        42.44        31.56 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        8.55        53.26        43.04         0.46         0.10         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
       26.89         4.54         4.14        13.58         5.88 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.07               0.07 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             18.51              53.26 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              9.70              13.58 
[1] "0.1 - 18.5 (9.7)"  "0.1 - 53.3 (13.6)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18Q LOSS CNV" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "18Q LOSS CNV" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
      "18Q LOSS CNV" 
[1] "hr=" "4.5"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          2    3
  18Q LOSS WILD-TYPE    8    9
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE            2                  8
  MALE              3                  9

Clustering(45) Variable = 19q loss
D45V1, survival
                    sevent
clus2                 0  1
  19Q LOSS CNV        1  2
  19Q LOSS WILD-TYPE 15  4
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 3                 19 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
                 2                  4 
$`19Q LOSS CNV`
TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-FX-A48G 
       18.51         9.70         0.07 

$`19Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        27.19        12.85        24.49        46.68        42.44 
TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
       31.56         8.55        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 
        0.07        26.89         4.54         4.14        13.58         5.88 
TCGA-KF-A41W 
        5.95 

      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              0.07               0.07 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
             18.51              53.26 
      19Q LOSS CNV 19Q LOSS WILD-TYPE 
              9.70              12.85 
[1] "0.1 - 18.5 (9.7)"  "0.1 - 53.3 (12.8)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"19Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"19Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"19Q LOSS WILD-TYPE"       "19Q LOSS CNV" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "19Q LOSS CNV" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" "19Q LOSS WILD-TYPE" 
        TCGA-KF-A41W 
"19Q LOSS WILD-TYPE" 
[1] "hr=" "3.7"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS CNV          1    2
  19Q LOSS WILD-TYPE    9   10
        clus
vv       19Q LOSS CNV 19Q LOSS WILD-TYPE
  FEMALE            1                  9
  MALE              2                 10

Clustering(46) Variable = 22q loss
D46V1, survival
                    sevent
clus2                 0  1
  22Q LOSS CNV        3  1
  22Q LOSS WILD-TYPE 13  5
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 4                 18 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 1                  5 
$`22Q LOSS CNV`
TCGA-DX-A1L2 TCGA-DX-A2IZ TCGA-FX-A48G TCGA-IW-A3M5 
       42.44         8.55         0.07         5.88 

$`22Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        27.19        12.85        24.49        18.51        46.68 
TCGA-DX-A1L3 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ 
       31.56         9.70        53.26        43.04         0.46         0.10 
TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-KF-A41W 
        0.07        26.89         4.54         4.14        13.58         5.95 

      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              0.07               0.07 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             42.44              53.26 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             7.215             13.215 
[1] "0.1 - 42.4 (7.2)"  "0.1 - 53.3 (13.2)"
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-KF-A41W 
"22Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-KF-A41W 
"22Q LOSS WILD-TYPE" 
        TCGA-DX-A1KW         TCGA-DX-A1KX         TCGA-DX-A1KY 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1KZ         TCGA-DX-A1L0         TCGA-DX-A1L1 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DX-A1L2         TCGA-DX-A1L3         TCGA-DX-A2IZ 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-DX-A2J0         TCGA-DX-A2J1         TCGA-DX-A2J4 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A2QS         TCGA-FX-A3NJ         TCGA-FX-A3RE 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FX-A48G         TCGA-HB-A2OT         TCGA-HB-A3YV 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-HB-A43Z         TCGA-IS-A3KA         TCGA-IW-A3M5 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-KF-A41W 
"22Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          2    2
  22Q LOSS WILD-TYPE    8   10
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  FEMALE            2                  8
  MALE              2                 10

Clustering(47) Variable = Xq loss
D47V1, survival
                   sevent
clus2                0  1
  XQ LOSS CNV        2  2
  XQ LOSS WILD-TYPE 14  4
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                4                18 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
                2                 4 
$`XQ LOSS CNV`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       27.19        12.85        18.51        46.68 

$`XQ LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A2IZ TCGA-DX-A2J0 
        2.04        24.49        42.44        31.56         8.55         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       53.26        43.04         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W 
       26.89         4.54         4.14        13.58         5.88         5.95 

      XQ LOSS CNV XQ LOSS WILD-TYPE 
            12.85              0.07 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            46.68             53.26 
      XQ LOSS CNV XQ LOSS WILD-TYPE 
            22.85              7.25 
[1] "12.8 - 46.7 (22.9)" "0.1 - 53.3 (7.2)"  
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A1KW        TCGA-DX-A1KX        TCGA-DX-A1KY        TCGA-DX-A1KZ 
"XQ LOSS WILD-TYPE"       "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A1L0        TCGA-DX-A1L1        TCGA-DX-A1L2        TCGA-DX-A1L3 
      "XQ LOSS CNV"       "XQ LOSS CNV" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-DX-A2IZ        TCGA-DX-A2J0        TCGA-DX-A2J1        TCGA-DX-A2J4 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-FX-A2QS        TCGA-FX-A3NJ        TCGA-FX-A3RE        TCGA-FX-A48G 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-HB-A2OT        TCGA-HB-A3YV        TCGA-HB-A43Z        TCGA-IS-A3KA 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
       TCGA-IW-A3M5        TCGA-KF-A41W 
"XQ LOSS WILD-TYPE" "XQ LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS CNV          1    3
  XQ LOSS WILD-TYPE    9    9
        clus
vv       XQ LOSS CNV XQ LOSS WILD-TYPE
  FEMALE           1                 9
  MALE             3                 9
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
