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

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> source("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/CNV2ClinicalAnalysis_nozzle_onlysig.R")
> result <- main("/xchip/tcga/gdac_prod/applications/tcga-gdac-genepattern/gp-3.2.4-9272/Tomcat/../../taskLib/Correlate_Clinical_Cnvsarms_onlysig.11.3769/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac-genepattern/jobResults/163235/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC/1669677/1.GDAC_clinicalDataPicker.Finished/LIHC.clin.merged.picked.txt", "-fF=ALL", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LIHC", "-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=LIHC"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=62, in cluster file=82, common to both=58
[1] "Reduce the number of clustering variables from 80 to 61."
[1] 61 58
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                49 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                9                49 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                26 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                26 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                50 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                50 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                51 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                51 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                54 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                54 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               18                40 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               18                40 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               13                45 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               13                45 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                45 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                45 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                50 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                50 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                40 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                40 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                39 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                39 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                47 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                47 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                29 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29                29 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                55 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                55 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                55 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                55 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 53 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 53 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 55 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 55 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 53 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 53 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 55 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 55 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 55 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 55 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 42 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 42 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 55 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 55 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 53 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 53 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 51 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 51 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 46 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 45 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 45 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 54 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 54 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 52 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 52 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                54 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                54 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                48 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               10                48 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                55 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                55 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                55 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                3                55 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                53 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                53 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                55 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                55 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                49 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                49 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                44 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                44 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                54 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                54 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                9                49 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                9                49 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                54 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4                54 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                51 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                51 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               25                33 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               25                33 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                51 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                7                51 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                45 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                45 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                47 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                47 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 55 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 55 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 46 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 46 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 53 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 53 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 50 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 50 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 54 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 54 
[1] "12q loss mutation analysis"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 55 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 55 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 38 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                20                 38 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 39 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 39 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 51 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 51 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                 47 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                 47 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                 40 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                18                 40 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                24                 34 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                24                 34 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 51 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 51 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 49 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 49 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 55 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 55 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 50 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 8                 50 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 9                 49 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 9                 49 
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "NEOADJUVANTTHERAPY"               "BATCHNUMBER"                     

Input Data has 12 rows and 58 columns.

[1] "Batch" "12"   
[1] "Last Follow UP"
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
          NA          352           NA           NA           NA           NA 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
          NA         1144          420            8          252            2 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 TCGA-CC-5264 TCGA-CC-A1HT 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
         217           NA           NA           NA          693           NA 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
          79           NA          652           NA           NA          601 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
          NA          129          110          111           60           NA 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
          97           NA           NA           NA           37         1175 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1231          434          390         1359           NA          269 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
         253          179          136           27 
Variable 1:'AGE':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'NEOADJUVANT.THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 12:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER"
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 58 columns, 1 survival variables, and 2 non-survival variables.
AGE, nv=36, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    4  3
  1P GAIN WILD-TYPE 23 23
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                46 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                23 
$`1P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-EP-A12J TCGA-EP-A26S 
       37.32        27.52         2.99        37.61         4.24         3.62 
TCGA-G3-A25W 
       12.82 

$`1P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X 
       48.99        11.57        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29        22.78         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A2KA TCGA-EP-A2KB 
       51.25        90.67        19.76        13.64         3.65         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S 
        0.62         3.19        22.85        14.40        19.07         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       38.63        40.47        14.27        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.99              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            37.61             90.67 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           12.820            13.725 
[1] "3.0 - 37.6 (12.8)" "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1P GAIN MUTATED"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      3    6
  1P GAIN WILD-TYPE   18   31
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                18
  MALE                 6                31

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   17 12
  1Q GAIN WILD-TYPE 10 14
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29                24 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                14 
$`1Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52         2.99        23.34         5.03 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
       37.61         8.28         7.13        37.74        22.78         7.33 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       21.44        90.67        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25W 
        1.97         0.62         3.19        19.07         1.22        12.82 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK 
       44.68         8.84         8.32         4.47         0.89 

$`1Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        11.57        46.78        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A115 
       69.57        13.81         0.26         0.07         4.24        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EC TCGA-ES-A2HS 
       53.29         2.60         0.46        51.25        19.76        22.85 
TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CI 
       14.40        38.63        40.47        14.27        14.86         5.88 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.62              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            90.67             83.57 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             8.32             17.31 
[1] "0.6 - 90.7 (8.3)"  "0.1 - 83.6 (17.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK 
  "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK 
  "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-G3-A3CK 
  "1Q GAIN MUTATED" 
[1] "hr=" "1.2"
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      9   23
  1Q GAIN WILD-TYPE   12   14
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE               9                12
  MALE                23                14

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  5
  2P GAIN WILD-TYPE 24 21
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                45 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                21 
$`2P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-ES-A2HS TCGA-G3-A25T 
       48.99        37.32        10.13        27.52        22.85        38.63 
TCGA-G3-A25W TCGA-G3-A25Z 
       12.82         8.84 

$`2P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       11.57        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        37.61        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29        22.78         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       51.25        90.67        19.76        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        3.65         1.97         0.62         3.19        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
        1.22        40.47        14.27        44.68        14.86         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.84              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            48.99             90.67 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           25.185            11.570 
[1] "8.8 - 49.0 (25.2)" "0.1 - 90.7 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      5    3
  2P GAIN WILD-TYPE   16   34
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5                16
  MALE                 3                34

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    3  4
  2Q GAIN WILD-TYPE 24 22
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                46 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                22 
$`2Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W 
       48.99        37.32        10.13        22.85        38.63        12.82 
TCGA-G3-A25Z 
        8.84 

$`2Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24         7.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
        3.62         3.65         1.97         0.62         3.19        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       19.07         1.22        40.47        14.27        44.68        14.86 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.84              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            48.99             90.67 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           22.850            12.605 
[1] "8.8 - 49.0 (22.9)" "0.1 - 90.7 (12.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      5    2
  2Q GAIN WILD-TYPE   16   35
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                16
  MALE                 2                35

Clustering(5) Variable = 4p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    2  1
  4P GAIN WILD-TYPE 25 25
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                3                50 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                25 
$`4P GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A118 TCGA-DD-A1EC 
       10.13        22.78        19.76 

$`4P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        7.13        37.74        83.57        53.29         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J 
        0.46        21.44        51.25        90.67        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.13              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            22.78             90.67 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            19.76             13.23 
[1] "10.1 - 22.8 (19.8)" "0.1 - 90.7 (13.2)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" "4P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3    1
  4P GAIN WILD-TYPE   18   36
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3                18
  MALE                 1                36

Clustering(6) Variable = 5p gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    7 10
  5P GAIN WILD-TYPE 20 16
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17                36 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               10                16 
$`5P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A115 
       37.32         2.99         5.03         8.28         4.24        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-EP-A2KB TCGA-EP-A3JL 
       53.29        22.78        51.25        90.67         1.97         3.19 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       14.40        19.07        12.82        44.68         8.32 

$`5P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A 
        0.26         0.07         7.13        37.74         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
        0.46        21.44        19.76        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        3.65         0.62        22.85         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.27        14.86         8.84         5.88         4.47         0.89 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.97              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            90.67             69.57 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           14.400            12.605 
[1] "2.0 - 90.7 (14.4)" "0.1 - 69.6 (12.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      6   12
  5P GAIN WILD-TYPE   15   25
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               6                15
  MALE                12                25

Clustering(7) Variable = 5q gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    4  8
  5Q GAIN WILD-TYPE 23 18
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               12                41 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                18 
$`5Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       37.32         2.99         5.03        83.57        53.29        22.78 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-EP-A2KB TCGA-ES-A2HT TCGA-G3-A25W TCGA-G3-A3CG 
       51.25        90.67         1.97        14.40        12.82         8.32 

$`5Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24         7.13        37.74 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1EL 
        7.33         2.60         0.46        21.44        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         3.19        22.85 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
       19.07         1.22        38.63        40.47        14.27        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         5.88         4.47         0.89 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.97              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            90.67             69.57 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            18.59             11.57 
[1] "2.0 - 90.7 (18.6)" "0.1 - 69.6 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      5    8
  5Q GAIN WILD-TYPE   16   29
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                16
  MALE                 8                29

Clustering(8) Variable = 6p gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    7  5
  6P GAIN WILD-TYPE 20 21
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               12                41 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                21 
$`6P GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A119 
       27.52        13.81         0.26         8.28         4.24         7.33 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A3CG 
        1.97         0.62        22.85         1.22        44.68         8.32 

$`6P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
       37.61         0.07         7.13        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       22.78         2.60         0.46        21.44        51.25        90.67 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       19.76        13.64         4.24         3.62         3.65         3.19 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         5.88         4.47         0.89 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.26              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            44.68             90.67 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            7.805            14.400 
[1] "0.3 - 44.7 (7.8)"  "0.1 - 90.7 (14.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" 
[1] "hr=" "2"  
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4    9
  6P GAIN WILD-TYPE   17   28
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               4                17
  MALE                 9                28

Clustering(9) Variable = 6q gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    4  3
  6Q GAIN WILD-TYPE 23 23
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                7                46 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                23 
$`6Q GAIN MUTATED`
TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A119 TCGA-EP-A2KB TCGA-EP-A2KC TCGA-G3-A25S 
        8.28         4.24         7.33         1.97         0.62         1.22 
TCGA-G3-A3CG 
        8.32 

$`6Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5258 TCGA-DD-A113 
        5.03        37.61        13.81         0.26         0.07         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        3.62         3.65         3.19        22.85        14.40        19.07 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       38.63        40.47        14.27        12.82        44.68        14.86 
TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         5.88         4.47         0.89 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.62              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             8.32             90.67 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             4.24             14.63 
[1] "0.6 - 8.3 (4.2)"   "0.1 - 90.7 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" 
[1] "hr=" "6.2"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      2    6
  6Q GAIN WILD-TYPE   19   31
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                19
  MALE                 6                31

Clustering(10) Variable = 7p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    9  6
  7P GAIN WILD-TYPE 18 20
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                38 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                20 
$`7P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A3KF TCGA-DD-A113 TCGA-DD-A118 
       37.32        10.13        27.52         0.26         7.13        22.78 
TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EC TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        2.60        51.25        19.76         0.62         3.19        22.85 
TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
       38.63         8.32         4.47 

$`7P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        8.28         0.07         4.24        37.74        83.57        53.29 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J 
        7.33         0.46        21.44        90.67        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S 
        3.62         3.65         1.97        14.40        19.07         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CI TCGA-G3-A3CK 
        5.88         0.89 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.26              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            51.25             90.67 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           10.130            13.725 
[1] "0.3 - 51.2 (10.1)" "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK 
"7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK 
"7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED"   "7P GAIN MUTATED"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-G3-A3CK 
"7P GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      9    9
  7P GAIN WILD-TYPE   12   28
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               9                12
  MALE                 9                28

Clustering(11) Variable = 7q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   10  6
  7Q GAIN WILD-TYPE 17 20
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                20 
$`7Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A3KF TCGA-DD-A118 TCGA-DD-A11A 
       37.32        10.13        27.52         0.26        22.78         2.60 
TCGA-DD-A11D TCGA-DD-A1EC TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       51.25        19.76         3.62         3.65         0.62         3.19 
TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
       22.85        38.63         8.32         4.47 

$`7Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EL 
       53.29         7.33         0.46        21.44        90.67        13.64 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U 
        4.24         1.97        14.40        19.07         1.22        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CI 
       14.27        12.82        44.68        14.86         8.84         5.88 
TCGA-G3-A3CK 
        0.89 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.26              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            51.25             90.67 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            9.225            13.810 
[1] "0.3 - 51.2 (9.2)"  "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"7Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      9   10
  7Q GAIN WILD-TYPE   12   27
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               9                12
  MALE                10                27

Clustering(12) Variable = 8p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    7  3
  8P GAIN WILD-TYPE 20 23
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10                43 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                23 
$`8P GAIN MUTATED`
TCGA-BC-A10S TCGA-CC-5258 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EC 
       46.78         0.07         7.33         2.60        90.67        19.76 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-G3-A25X TCGA-G3-A25Z 
        1.97         3.19        44.68         8.84 

$`8P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A113 
       37.61        13.81         0.26         8.28         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       37.74        83.57        53.29        22.78         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       51.25        13.64         4.24         3.62         3.65         0.62 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.27        12.82        14.86         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.67             83.57 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            8.085            13.810 
[1] "0.1 - 90.7 (8.1)"  "0.3 - 83.6 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" 
[1] "hr=" "3.1"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      2    9
  8P GAIN WILD-TYPE   19   28
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               2                19
  MALE                 9                28

Clustering(13) Variable = 8q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   17 10
  8Q GAIN WILD-TYPE 10 16
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               27                26 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               10                16 
$`8Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF TCGA-CC-5258 
       48.99        46.78        27.52         2.99         0.26         0.07 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
        7.13        53.29        22.78         7.33         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       90.67        19.76         4.24         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X 
        3.19        22.85        14.40        38.63        12.82        44.68 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
        8.84         8.32         4.47 

$`8Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y 
       11.57        37.32        10.13        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        37.61        13.81         8.28 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EL 
        4.24        37.74        83.57         0.46        51.25        13.64 
TCGA-EP-A26S TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y 
        3.62        19.07         1.22        40.47        14.27        14.86 
TCGA-G3-A3CI TCGA-G3-A3CK 
        5.88         0.89 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            90.67             83.57 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             8.84             14.04 
[1] "0.1 - 90.7 (8.8)"  "0.5 - 83.6 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-G3-A3CK 
"8Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      9   20
  8Q GAIN WILD-TYPE   12   17
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE               9                12
  MALE                20                17

Clustering(14) Variable = 9p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 25 26
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                26 
$`9P GAIN MUTATED`
TCGA-EP-A2KB TCGA-G3-A25U 
        1.97        40.47 

$`9P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24         7.13        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.44        51.25        90.67 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       19.76        13.64         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        3.19        22.85        14.40        19.07         1.22        38.63 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.97              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            40.47             90.67 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            21.22             13.64 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                51 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25V        TCGA-G3-A25W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2    1
  9P GAIN WILD-TYPE   19   36
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                19
  MALE                 1                36

Clustering(15) Variable = 9q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    2  0
  9Q GAIN WILD-TYPE 25 26
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                51 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                26 
$`9Q GAIN MUTATED`
TCGA-EP-A2KB TCGA-G3-A25U 
        1.97        40.47 

$`9Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24         7.13        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.44        51.25        90.67 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       19.76        13.64         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        3.19        22.85        14.40        19.07         1.22        38.63 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.97              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            40.47             90.67 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            21.22             13.64 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                51 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25V        TCGA-G3-A25W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2    1
  9Q GAIN WILD-TYPE   19   36
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                19
  MALE                 1                36

Clustering(16) Variable = 10p gain mutation analysis
D16V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    1  3
  10P GAIN WILD-TYPE 26 23
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 49 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 23 
$`10P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-EP-A2KB TCGA-ES-A2HS 
       37.32        10.13         1.97        22.85 

$`10P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        11.57        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        0.46        21.44        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
        4.24         3.62         3.65         0.62         3.19        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         1.22        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.97               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             37.32              90.67 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             16.49              13.64 
[1] "2.0 - 37.3 (16.5)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D16V2, continuous
D16V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    2
  10P GAIN WILD-TYPE   18   35
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                  2                 35

Clustering(17) Variable = 12q gain mutation analysis
D17V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  0
  12Q GAIN WILD-TYPE 25 26
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 51 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                 26 
$`12Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-G3-A25T 
        0.26        38.63 

$`12Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61        13.81         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        2.60         0.46        21.44        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.64         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U 
        3.19        22.85        14.40        19.07         1.22        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.26               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             38.63              90.67 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.445             13.640 
[1] "0.3 - 38.6 (19.4)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 51 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-CC-5258         TCGA-CC-5263 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-EP-A12J         TCGA-EP-A26S 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25U 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
D17V2, continuous
D17V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    1
  12Q GAIN WILD-TYPE   19   36
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                  1                 36

Clustering(18) Variable = 15q gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  3
  15Q GAIN WILD-TYPE 25 23
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 48 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 23 
$`15Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-ES-A2HS TCGA-G3-A25T 
       37.32        23.34         8.28        22.85        38.63 

$`15Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
       13.81         0.26         0.07         4.24         7.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT 
        3.62         3.65         1.97         0.62         3.19        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07         1.22        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.28               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             38.63              90.67 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            23.340             12.195 
[1] "8.3 - 38.6 (23.3)" "0.1 - 90.7 (12.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   18   35
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                  2                 35

Clustering(19) Variable = 16p gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  2
  16P GAIN WILD-TYPE 26 24
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 50 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 24 
$`16P GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A11A 
       10.13         5.03         2.60 

$`16P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.60               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             10.13              90.67 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5.03              14.04 
[1] "2.6 - 10.1 (5.0)"  "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "6.5"
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   20   35
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                  2                 35

Clustering(20) Variable = 17p gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    1  2
  17P GAIN WILD-TYPE 26 24
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 50 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 24 
$`17P GAIN MUTATED`
TCGA-BC-A10Q TCGA-EP-A2KB TCGA-ES-A2HS 
       37.32         1.97        22.85 

$`17P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        2.60         0.46        21.44        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       13.64         4.24         3.62         3.65         0.62         3.19 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.97               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             37.32              90.67 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             22.85              13.23 
[1] "2.0 - 37.3 (22.9)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "1.7"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    1
  17P GAIN WILD-TYPE   19   36
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 19
  MALE                  1                 36

Clustering(21) Variable = 17q gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    6  9
  17Q GAIN WILD-TYPE 21 17
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                15                 38 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 17 
$`17Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       48.99        37.32         2.99        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-CC-5263 TCGA-DD-A114 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25U 
       13.81         4.24        37.74         1.97        22.85        40.47 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK 
       12.82         8.84         0.89 

$`17Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X 
       11.57        10.13        46.78        27.52        27.52        25.32 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A113 
       69.57        37.61         0.26         8.28         0.07         7.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        3.62         3.65         0.62         3.19        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
        1.22        38.63        14.27        44.68        14.86         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ 
        5.88         4.47 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.89               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             48.99              90.67 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            12.820             13.955 
[1] "0.9 - 49.0 (12.8)" "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "2.1"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7    9
  17Q GAIN WILD-TYPE   14   28
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                7                 14
  MALE                  9                 28

Clustering(22) Variable = 18q gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  1
  18Q GAIN WILD-TYPE 25 25
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 50 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 25 
$`18Q GAIN MUTATED`
TCGA-CC-5263 TCGA-DD-A113 TCGA-G3-A25X 
        4.24         7.13        44.68 

$`18Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        0.46        21.44        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       14.27        12.82        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              4.24               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             44.68              90.67 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             7.130             13.725 
[1] "4.2 - 44.7 (7.1)"  "0.1 - 90.7 (13.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q GAIN WILD-TYPE"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   20   35
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 20
  MALE                  2                 35

Clustering(23) Variable = 19p gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    4  1
  19P GAIN WILD-TYPE 23 25
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 48 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 25 
$`19P GAIN MUTATED`
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
        7.13        22.78        19.76         1.97        22.85 

$`19P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        4.24        37.74        83.57        53.29         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J 
        0.46        21.44        51.25        90.67        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        3.62         3.65         0.62         3.19        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.97               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             22.85              90.67 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             19.76              13.23 
[1] "2.0 - 22.9 (19.8)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19P GAIN MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "1.4"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    1
  19P GAIN WILD-TYPE   17   36
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                 17
  MALE                  1                 36

Clustering(24) Variable = 19q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    5  2
  19Q GAIN WILD-TYPE 22 24
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 46 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 24 
$`19Q GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       10.13         7.13        22.78        19.76         1.97        22.85 
TCGA-G3-A25X 
       44.68 

$`19Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       21.44        51.25        90.67        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S 
        3.65         0.62         3.19        14.40        19.07         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       38.63        40.47        14.27        12.82        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.97               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             44.68              90.67 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             19.76              13.23 
[1] "2.0 - 44.7 (19.8)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    2
  19Q GAIN WILD-TYPE   16   35
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                 16
  MALE                  2                 35

Clustering(25) Variable = 20p gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    5  5
  20P GAIN WILD-TYPE 22 21
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 43 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 21 
$`20P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-DD-A118 TCGA-DD-A11B 
       48.99        37.32        10.13         0.26        22.78         0.46 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
        1.97         3.19        22.85         1.22 

$`20P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.29         7.33         2.60        21.44        51.25        90.67 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       19.76        13.64         4.24         3.62         3.65         0.62 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.26               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             48.99              90.67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              6.66              13.81 
[1] "0.3 - 49.0 (6.7)"  "0.1 - 90.7 (13.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED"   "20P GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "1.8"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    6
  20P GAIN WILD-TYPE   15   31
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                6                 15
  MALE                  6                 31

Clustering(26) Variable = 20q gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    6  5
  20Q GAIN WILD-TYPE 21 21
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 42 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 21 
$`20Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-DD-A118 TCGA-DD-A11B 
       48.99        37.32        10.13         0.26        22.78         0.46 
TCGA-DD-A11C TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
       21.44         1.97         3.19        22.85         1.22 

$`20Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
       53.29         7.33         2.60        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT 
       13.64         4.24         3.62         3.65         0.62        14.40 
TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             48.99              90.67 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            10.130             13.725 
[1] "0.3 - 49.0 (10.1)" "0.1 - 90.7 (13.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED"   "20Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    7
  20Q GAIN WILD-TYPE   15   30
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 15
  MALE                  7                 30

Clustering(27) Variable = 21q gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 24 25
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 49 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 25 
$`21Q GAIN MUTATED`
TCGA-DD-A113 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25T 
        7.13         1.97        22.85        38.63 

$`21Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        4.24        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        2.60         0.46        21.44        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       13.64         4.24         3.62         3.65         0.62         3.19 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07         1.22        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.97               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             38.63              90.67 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             14.99              13.64 
[1] "2.0 - 38.6 (15.0)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   18   36
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                  1                 36

Clustering(28) Variable = 22q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    1  5
  22Q GAIN WILD-TYPE 26 21
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 6                 47 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 21 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A118 TCGA-DD-A11D TCGA-ES-A2HS TCGA-FV-A2QR 
       10.13         5.03        22.78        51.25        22.85        19.07 

$`22Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       21.44        90.67        19.76        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-G3-A25S 
        3.65         1.97         0.62         3.19        14.40         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       38.63        40.47        14.27        12.82        44.68        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         5.88         4.47         0.89 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              5.03               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             51.25              90.67 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            20.925             12.820 
[1] "5.0 - 51.2 (20.9)" "0.1 - 90.7 (12.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "2"  
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      3    3
  22Q GAIN WILD-TYPE   18   34
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                3                 18
  MALE                  3                 34

Clustering(29) Variable = Xq gain mutation analysis
D29V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 25 24
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                49 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                24 
$`XQ GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A10Z TCGA-DD-A11A TCGA-EP-A12J 
       27.52         1.12         2.60         4.24 

$`XQ GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A26S 
       21.44        51.25        90.67        19.76        13.64         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         1.22        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.12              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            27.52             90.67 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.42             13.81 
[1] "1.1 - 27.5 (3.4)"  "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" 
[1] "hr=" "2.5"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   20   34
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                20
  MALE                 3                34

Clustering(30) Variable = 1p loss mutation analysis
D30V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    4  5
  1P LOSS WILD-TYPE 23 21
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                9                44 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                21 
$`1P LOSS MUTATED`
TCGA-BC-A10S TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-EP-A2KB 
       46.78         7.13        22.78         0.46        51.25         1.97 
TCGA-EP-A2KC TCGA-ES-A2HS TCGA-G3-A25U 
        0.62        22.85        40.47 

$`1P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       37.74        83.57        53.29         7.33         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       90.67        19.76        13.64         4.24         3.62         3.65 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        3.19        14.40        19.07         1.22        38.63        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.46              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            51.25             90.67 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            22.78             13.23 
[1] "0.5 - 51.2 (22.8)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      5    5
  1P LOSS WILD-TYPE   16   32
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               5                16
  MALE                 5                32

Clustering(31) Variable = 1q loss mutation analysis
D31V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    1  2
  1Q LOSS WILD-TYPE 26 24
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                3                50 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                24 
$`1Q LOSS MUTATED`
TCGA-BC-A10S TCGA-ES-A2HS TCGA-G3-A25U 
       46.78        22.85        40.47 

$`1Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        2.60         0.46        21.44        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.64         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        3.19        14.40        19.07         1.22        38.63        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            22.85              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            46.78             90.67 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           40.470            12.195 
[1] "22.9 - 46.8 (40.5)" "0.1 - 90.7 (12.2)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      1    2
  1Q LOSS WILD-TYPE   20   35
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               1                20
  MALE                 2                35

Clustering(32) Variable = 2q loss mutation analysis
D32V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 25 26
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                51 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                26 
$`2Q LOSS MUTATED`
TCGA-BC-A3KF TCGA-DD-A11C 
        0.26        21.44 

$`2Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61        13.81         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        2.60         0.46        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.26              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            21.44             90.67 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            10.85             13.64 
[1] "0.3 - 21.4 (10.9)" "0.1 - 90.7 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                51 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113        TCGA-DD-A114 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11D        TCGA-DD-A1E9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-G3-A25S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V        TCGA-G3-A25W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      1    2
  2Q LOSS WILD-TYPE   20   35
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               1                20
  MALE                 2                35

Clustering(33) Variable = 3p loss mutation analysis
D33V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 24 24
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                48 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                24 
$`3P LOSS MUTATED`
TCGA-BC-A112 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A118 TCGA-G3-A25T 
        5.03         4.24         7.13        22.78        38.63 

$`3P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A114 
       37.61        13.81         0.26         8.28         0.07        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       51.25        90.67        19.76        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07         1.22        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             4.24              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            38.63             90.67 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            7.130            13.725 
[1] "4.2 - 38.6 (7.1)"  "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE   18   35
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 2                35

Clustering(34) Variable = 3q loss mutation analysis
D34V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 25 25
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                50 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                25 
$`3Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 
        5.03         7.13        22.78 

$`3Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             5.03              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            22.78             90.67 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            7.130            13.725 
[1] "5.0 - 22.8 (7.1)"  "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3Q LOSS MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   19   36
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                19
  MALE                 1                36

Clustering(35) Variable = 4p loss mutation analysis
D35V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    4  4
  4P LOSS WILD-TYPE 23 22
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                45 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                22 
$`4P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25U 
       23.34         5.03        13.64         1.97         1.22        40.47 
TCGA-G3-A25X TCGA-G3-A25Y 
       44.68        14.86 

$`4P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J 
        0.46        21.44        51.25        90.67        19.76         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
        3.62         3.65         0.62         3.19        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
       19.07        38.63        14.27        12.82         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.22              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            44.68             90.67 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.25             12.82 
[1] "1.2 - 44.7 (14.2)" "0.1 - 90.7 (12.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    6
  4P LOSS WILD-TYPE   18   31
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 6                31

Clustering(36) Variable = 4q loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    7  6
  4Q LOSS WILD-TYPE 20 20
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               13                40 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                20 
$`4Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A3KF TCGA-DD-A113 TCGA-DD-A116 
       27.52        23.34         5.03         0.26         7.13        53.29 
TCGA-DD-A11A TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y 
        2.60        13.64         1.97         1.22        44.68        14.86 
TCGA-G3-A25Z 
        8.84 

$`4Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32         1.12        69.57        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        8.28         0.07         4.24        37.74        83.57        22.78 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        7.33         0.46        21.44        51.25        90.67        19.76 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.26              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            53.29             90.67 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             8.84             14.04 
[1] "0.3 - 53.3 (8.8)"  "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      4   10
  4Q LOSS WILD-TYPE   17   27
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               4                17
  MALE                10                27

Clustering(37) Variable = 5q loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    1  3
  5Q LOSS WILD-TYPE 26 23
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                49 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                23 
$`5Q LOSS MUTATED`
TCGA-BC-A10R TCGA-CC-5263 TCGA-ES-A2HS TCGA-G3-A25S 
       10.13         4.24        22.85         1.22 

$`5Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A113 
       37.61        13.81         0.26         8.28         0.07         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        0.46        21.44        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.22              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            22.85             90.67 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            7.185            13.810 
[1] "1.2 - 22.9 (7.2)"  "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" 
[1] "hr=" "4.7"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    3
  5Q LOSS WILD-TYPE   20   34
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               1                20
  MALE                 3                34

Clustering(38) Variable = 6q loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    6  2
  6Q LOSS WILD-TYPE 21 24
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                8                45 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                24 
$`6Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EC TCGA-EP-A12J TCGA-FV-A2QR 
       37.32        22.78        21.44        19.76         4.24        19.07 
TCGA-G3-A25T TCGA-G3-A25X 
       38.63        44.68 

$`6Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        7.13        37.74        83.57        53.29         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A26S TCGA-EP-A2KA 
        0.46        51.25        90.67        13.64         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-G3-A25S 
        1.97         0.62         3.19        22.85        14.40         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       40.47        14.27        12.82        14.86         8.84         8.32 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             4.24              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            44.68             90.67 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            22.11             10.13 
[1] "4.2 - 44.7 (22.1)" "0.1 - 90.7 (10.1)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" 
[1] "hr=" "2.3"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    4
  6Q LOSS WILD-TYPE   16   33
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               5                16
  MALE                 4                33

Clustering(39) Variable = 7p loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  0
  7P LOSS WILD-TYPE 24 26
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                50 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                26 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-EP-A2KB 
       13.81         8.28         1.97 

$`7P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
        5.03        37.61         0.26         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        0.46        21.44        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.97              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.81             90.67 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            8.280            13.955 
[1] "2.0 - 13.8 (8.3)"  "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" 
[1] "hr="     "2.6e+07"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    1
  7P LOSS WILD-TYPE   18   36
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 1                36

Clustering(40) Variable = 7q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    4  2
  7Q LOSS WILD-TYPE 23 24
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                47 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                24 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S 
       48.99        13.81         8.28        13.64         1.97         1.22 

$`7Q LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       11.57        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
       37.61         0.26         0.07         4.24         7.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S 
       21.44        51.25        90.67        19.76         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        3.65         0.62         3.19        22.85        14.40        19.07 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
       38.63        40.47        14.27        12.82        44.68        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         5.88         4.47         0.89 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.22              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            48.99             90.67 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.96             14.27 
[1] "1.2 - 49.0 (11.0)" "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    3
  7Q LOSS WILD-TYPE   17   34
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               4                17
  MALE                 3                34

Clustering(41) Variable = 8p loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   10 13
  8P LOSS WILD-TYPE 17 13
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               23                30 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                13 
$`8P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A216 
       48.99        37.32        10.13        27.52         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       13.81         8.28         7.13        83.57        53.29        22.78 
TCGA-DD-A11C TCGA-DD-A1EL TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HS 
       21.44        13.64         3.62         3.65         0.62        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A3CJ 
       14.40        19.07         1.22        14.86         4.47 

$`8P LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       11.57        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 
        1.12        69.57         0.26         0.07         4.24        37.74 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        7.33         2.60         0.46        51.25        90.67        19.76 
TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3JL TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        4.24         1.97         3.19        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CK 
       12.82        44.68         8.84         8.32         5.88         0.89 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.62              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            83.57             90.67 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           14.400            10.205 
[1] "0.6 - 83.6 (14.4)" "0.1 - 90.7 (10.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK 
"8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK 
"8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-G3-A3CK 
"8P LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     10   15
  8P LOSS WILD-TYPE   11   22
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              10                11
  MALE                15                22

Clustering(42) Variable = 8q loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    3  2
  8Q LOSS WILD-TYPE 24 24
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                48 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                24 
$`8Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-EP-A26S TCGA-G3-A25Y 
       27.52        13.81         8.28         3.62        14.86 

$`8Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
       37.61         0.26         0.07         4.24         7.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       83.57        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         1.22        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       44.68         8.84         8.32         5.88         4.47         0.89 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             3.62              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            27.52             90.67 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            13.81             13.23 
[1] "3.6 - 27.5 (13.8)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    4
  8Q LOSS WILD-TYPE   18   33
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 4                33

Clustering(43) Variable = 9p loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    6  7
  9P LOSS WILD-TYPE 21 19
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               13                40 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                19 
$`9P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 
       48.99        10.13        27.52         5.03         0.07         7.13 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-G3-A25S 
       83.57        53.29         2.60         0.46        21.44         1.22 
TCGA-G3-A25T 
       38.63 

$`9P LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       11.57        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57        37.61        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D 
        8.28         4.24        37.74        22.78         7.33        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       90.67        19.76        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        1.97         0.62         3.19        22.85        14.40        19.07 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.26 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.57             90.67 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           10.130            13.725 
[1] "0.1 - 83.6 (10.1)" "0.3 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      4    9
  9P LOSS WILD-TYPE   17   28
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               4                17
  MALE                 9                28

Clustering(44) Variable = 9q loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    6  5
  9Q LOSS WILD-TYPE 21 21
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               11                42 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                21 
$`9Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A116 
       10.13        27.52         5.03         0.07         7.13        53.29 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-G3-A25S TCGA-G3-A25T 
        2.60         0.46        21.44         1.22        38.63 

$`9Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       48.99        11.57        37.32        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.26         8.28         4.24        37.74        83.57        22.78 
TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
        7.33        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       14.40        19.07        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.26 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            53.29             90.67 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             7.13             14.04 
[1] "0.1 - 53.3 (7.1)"  "0.3 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EC        TCGA-DD-A1EL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CI        TCGA-G3-A3CJ 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      3    8
  9Q LOSS WILD-TYPE   18   29
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               3                18
  MALE                 8                29

Clustering(45) Variable = 10p loss mutation analysis
D45V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2  1
  10P LOSS WILD-TYPE 25 25
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 50 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 25 
$`10P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A112 TCGA-DD-A11C 
       11.57         5.03        21.44 

$`10P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
        0.46        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              5.03               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             21.44              90.67 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            11.570             13.725 
[1] "5.0 - 21.4 (11.6)" "0.1 - 90.7 (13.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    3
  10P LOSS WILD-TYPE   21   34
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                0                 21
  MALE                  3                 34

Clustering(46) Variable = 10q loss mutation analysis
D46V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5  5
  10Q LOSS WILD-TYPE 22 21
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 43 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
$`10Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       11.57        37.32        10.13         2.99         5.03        13.81 
TCGA-DD-A11C TCGA-DD-A1EL TCGA-G3-A25U TCGA-G3-A25X 
       21.44        13.64        40.47        44.68 

$`10Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        46.78        27.52        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        1.12        69.57        37.61         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24         7.13        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
        7.33         2.60         0.46        51.25        90.67        19.76 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
       22.85        14.40        19.07         1.22        38.63        14.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       12.82        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.99               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             44.68              90.67 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.725             12.820 
[1] "3.0 - 44.7 (13.7)" "0.1 - 90.7 (12.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    7
  10Q LOSS WILD-TYPE   16   30
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                5                 16
  MALE                  7                 30

Clustering(47) Variable = 11p loss mutation analysis
D47V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    2  3
  11P LOSS WILD-TYPE 25 23
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 48 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 23 
$`11P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-DD-A113 TCGA-DD-A115 
       37.32         5.03        13.81         7.13        83.57 

$`11P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A116 
        0.26         8.28         0.07         4.24        37.74        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       22.78         7.33         2.60         0.46        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       90.67        19.76        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        1.97         0.62         3.19        22.85        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.03               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             83.57              90.67 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             13.81              13.23 
[1] "5.0 - 83.6 (13.8)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    2
  11P LOSS WILD-TYPE   18   35
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                 18
  MALE                  2                 35

Clustering(48) Variable = 11q loss mutation analysis
D48V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    4  3
  11Q LOSS WILD-TYPE 23 23
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 46 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 23 
$`11Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5263 TCGA-DD-A113 
       11.57        37.32         5.03        13.81         4.24         7.13 
TCGA-G3-A25S 
        1.22 

$`11Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        10.13        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57        37.61         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.28         0.07        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.44        51.25        90.67 
TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       19.76        13.64         4.24         3.62         3.65         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T 
        0.62         3.19        22.85        14.40        19.07        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.22               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             37.32              90.67 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             7.130             14.335 
[1] "1.2 - 37.3 (7.1)"  "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D48V2, continuous
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    5
  11Q LOSS WILD-TYPE   18   32
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                 18
  MALE                  5                 32

Clustering(49) Variable = 12p loss mutation analysis
D49V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 23 26
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 49 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                 26 
$`12P LOSS MUTATED`
TCGA-BC-A217 TCGA-DD-A1EC TCGA-G3-A25S TCGA-G3-A25Z 
       13.81        19.76         1.22         8.84 

$`12P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL 
        2.60         0.46        21.44        51.25        90.67        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       22.85        14.40        19.07        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       12.82        44.68        14.86         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.22               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             19.76              90.67 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            11.325             13.640 
[1] "1.2 - 19.8 (11.3)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12P LOSS MUTATED" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    2
  12P LOSS WILD-TYPE   19   35
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 19
  MALE                  2                 35

Clustering(50) Variable = 12q loss mutation analysis
D50V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED    3  0
  12Q LOSS WILD-TYPE 24 26
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 3                 50 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 0                 26 
$`12Q LOSS MUTATED`
TCGA-BC-A217 TCGA-DD-A1EC TCGA-G3-A25Z 
       13.81        19.76         8.84 

$`12Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EL 
        2.60         0.46        21.44        51.25        90.67        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CI 
       14.27        12.82        44.68        14.86         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              8.84               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             19.76              90.67 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             13.81              13.23 
[1] "8.8 - 19.8 (13.8)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"   "12Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "12Q LOSS MUTATED" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      2    1
  12Q LOSS WILD-TYPE   19   36
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                2                 19
  MALE                  1                 36

Clustering(51) Variable = 13q loss mutation analysis
D51V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   10  6
  13Q LOSS WILD-TYPE 17 20
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                16                 37 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 20 
$`13Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       37.32        10.13        27.52         5.03        13.81         8.28 
TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.07         7.13        83.57        53.29        22.78         2.60 
TCGA-DD-A11C TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
       21.44         1.22        38.63        44.68 

$`13Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5263 
       23.34         1.12        69.57        37.61         0.26         4.24 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
       37.74         7.33         0.46        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.64         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25U TCGA-G3-A25V 
        3.19        22.85        14.40        19.07        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       12.82        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.57              90.67 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            17.625             12.820 
[1] "0.1 - 83.6 (17.6)" "0.3 - 90.7 (12.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   12
  13Q LOSS WILD-TYPE   13   25
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 12                 25

Clustering(52) Variable = 14q loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   10  6
  14Q LOSS WILD-TYPE 17 20
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                16                 37 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 20 
$`14Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       37.32        10.13        27.52         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        8.28         0.07         7.13        22.78         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S 
       90.67        13.64         1.97         1.22 

$`14Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-CC-5263 TCGA-DD-A114 
       23.34         1.12        69.57        37.61         4.24        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EC 
       83.57        53.29         7.33         0.46        51.25        19.76 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             90.67              83.57 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             9.205             14.400 
[1] "0.1 - 90.7 (9.2)"  "0.5 - 83.6 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      8   11
  14Q LOSS WILD-TYPE   13   26
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 11                 26

Clustering(53) Variable = 15q loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    3  3
  15Q LOSS WILD-TYPE 24 23
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 47 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                 23 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25Z 
        5.03         7.13        83.57        13.64         1.97         8.84 

$`15Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S 
       21.44        51.25        90.67        19.76         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        3.65         0.62         3.19        22.85        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        1.22        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.32         5.88         4.47         0.89 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.97               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             83.57              90.67 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             7.985             14.270 
[1] "2.0 - 83.6 (8.0)"  "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    5
  15Q LOSS WILD-TYPE   19   32
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                2                 19
  MALE                  5                 32

Clustering(54) Variable = 16p loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    4  3
  16P LOSS WILD-TYPE 23 23
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                 46 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 23 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-CC-5258 TCGA-DD-A11B TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25X 
       13.81         0.07         0.46         1.97        22.85        44.68 
TCGA-G3-A25Y 
       14.86 

$`16P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A113 
        5.03        37.61         0.26         8.28         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J 
       21.44        51.25        90.67        19.76        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
        3.62         3.65         0.62         3.19        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z 
        1.22        38.63        40.47        14.27        12.82         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.26 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             44.68              90.67 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             13.81              13.23 
[1] "0.1 - 44.7 (13.8)" "0.3 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED"   "16P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      4    7
  16P LOSS WILD-TYPE   17   30
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                4                 17
  MALE                  7                 30

Clustering(55) Variable = 16q loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED    9  7
  16Q LOSS WILD-TYPE 18 19
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                 37 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 19 
$`16Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 
       46.78         2.99        37.61        13.81         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-EP-A2KB 
        4.24         7.13        53.29         2.60         0.46         1.97 
TCGA-ES-A2HS TCGA-G3-A25U TCGA-G3-A25X TCGA-G3-A25Y 
       22.85        40.47        44.68        14.86 

$`16Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A3KF 
       25.32        23.34         1.12        69.57         5.03         0.26 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.74        83.57        22.78         7.33        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       90.67        19.76        13.64         4.24         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        0.62         3.19        14.40        19.07         1.22        38.63 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.27        12.82         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.26 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             53.29              90.67 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            11.045             13.640 
[1] "0.1 - 53.3 (11.0)" "0.3 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      8   10
  16Q LOSS WILD-TYPE   13   27
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 10                 27

Clustering(56) Variable = 17p loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   10 12
  17P LOSS WILD-TYPE 17 14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                22                 31 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 14 
$`17P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF 
       11.57        10.13        27.52         1.12        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.28         0.07         4.24        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EL TCGA-EP-A2KC 
        7.33         2.60        21.44        51.25        13.64         0.62 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A25Z 
       19.07         1.22        14.86         8.84 

$`17P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        37.32        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-DD-A113 TCGA-DD-A114 
       23.34        69.57         5.03        37.61         7.13        37.74 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        0.46        90.67        19.76         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25U 
        1.97         3.19        22.85        14.40        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.27        12.82        44.68         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.46 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             83.57              90.67 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             10.85              14.40 
[1] "0.1 - 83.6 (10.9)" "0.5 - 90.7 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      8   16
  17P LOSS WILD-TYPE   13   21
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE                8                 13
  MALE                 16                 21

Clustering(57) Variable = 18p loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  4
  18P LOSS WILD-TYPE 24 22
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 46 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 22 
$`18P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-DD-A118 TCGA-DD-A11B TCGA-ES-A2HS 
       10.13         5.03        13.81        22.78         0.46        22.85 
TCGA-G3-A25S 
        1.22 

$`18P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24         7.13        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.29         7.33         2.60        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       90.67        19.76        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T 
        1.97         0.62         3.19        14.40        19.07        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.46               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             22.85              90.67 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            10.130             13.955 
[1] "0.5 - 22.9 (10.1)" "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "3.6"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    4
  18P LOSS WILD-TYPE   18   33
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                3                 18
  MALE                  4                 33

Clustering(58) Variable = 18q loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  4
  18Q LOSS WILD-TYPE 22 22
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 44 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 22 
$`18Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-DD-A118 TCGA-DD-A11A 
       10.13         5.03        37.61        13.81        22.78         2.60 
TCGA-DD-A11B TCGA-ES-A2HS TCGA-G3-A25S 
        0.46        22.85         1.22 

$`18Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF 
        2.99        25.32        23.34         1.12        69.57         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24         7.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC 
       53.29         7.33        21.44        51.25        90.67        19.76 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       13.64         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        3.19        14.40        19.07        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.46               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             37.61              90.67 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            10.130             13.955 
[1] "0.5 - 37.6 (10.1)" "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2"  
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    5
  18Q LOSS WILD-TYPE   17   32
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                4                 17
  MALE                  5                 32

Clustering(59) Variable = 19p loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    2  1
  19P LOSS WILD-TYPE 25 25
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 3                 50 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 25 
$`19P LOSS MUTATED`
TCGA-BC-A10W TCGA-DD-A11A TCGA-G3-A25S 
        2.99         2.60         1.22 

$`19P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
       27.52        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        7.13        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL 
        0.46        21.44        51.25        90.67        19.76        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
        4.24         3.62         3.65         1.97         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       22.85        14.40        19.07        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.22               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.99              90.67 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.60              14.04 
[1] "1.2 - 3.0 (2.6)"   "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"   "19P LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "6.4"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    3
  19P LOSS WILD-TYPE   21   34
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                0                 21
  MALE                  3                 34

Clustering(60) Variable = 21q loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    2  3
  21Q LOSS WILD-TYPE 25 23
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 5                 48 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 23 
$`21Q LOSS MUTATED`
TCGA-BC-A10U TCGA-BC-A112 TCGA-DD-A11A TCGA-DD-A1EL TCGA-G3-A25S 
       27.52         5.03         2.60        13.64         1.22 

$`21Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24         7.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-EP-A12J TCGA-EP-A26S 
       21.44        51.25        90.67        19.76         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         8.32         5.88         4.47         0.89 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.22               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             27.52              90.67 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              5.03              14.04 
[1] "1.2 - 27.5 (5.0)"  "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "3"  
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    8
  21Q LOSS WILD-TYPE   21   29
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                0                 21
  MALE                  8                 29

Clustering(61) Variable = 22q loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    5  2
  22Q LOSS WILD-TYPE 22 24
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                 46 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 24 
$`22Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-DD-A113 TCGA-EP-A2KB TCGA-G3-A25S 
       37.32        27.52        13.81         7.13         1.97         1.22 
TCGA-G3-A25T 
       38.63 

$`22Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W 
       48.99        11.57        10.13        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        37.61 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 
        0.26         8.28         0.07         4.24        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29        22.78         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       51.25        90.67        19.76        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        3.65         0.62         3.19        22.85        14.40        19.07 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         5.88         4.47         0.89 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1.22               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             38.63              90.67 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.81              13.23 
[1] "1.2 - 38.6 (13.8)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1EL         TCGA-EP-A12J 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A26S         TCGA-EP-A2KA         TCGA-EP-A2KB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-EP-A2KC         TCGA-EP-A3JL         TCGA-ES-A2HS 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
  "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    3
  22Q LOSS WILD-TYPE   15   34
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 15
  MALE                  3                 34
           V1.D              V2              V3 
"Time to Death"           "AGE"        "GENDER" 
> q(save="no")
