
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/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/CNV2ClinicalAnalysis_nozzle_onlysig_arm.R")
> result <- main("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/20/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/LIHC-TP/3472530/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/LIHC-TP/3351371/LIHC-TP.clin.merged.picked.txt", "-fF=", "-fC=3", "-fH=5", "-fW=9", "-fP=OUT", "-cP=1", "-cQ=0.25", "-MF=ONLYSIG", "-oT=LIHC-TP", "-nV=Nozzle.R1", "-OP=MUTSIG", "-iT=", "-iX=")
[1] "nver"          "-nV=Nozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"         "-oT=LIHC-TP"
[1] "opt"        "-OP=MUTSIG"
[1] "tl"   "-iT="
[1] "dx"   "-iX="
[1] "opt"    "MUTSIG"
[1] "dx" ""  

nPatients in clinical file=73, in cluster file=108, common to both=72
[1] "Reduce the number of clustering variables from 80 to 66."
[1] 66 72
[1] "1p gain"
[1] 3
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8                64 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                8                64 
[1] "1q gain"
[1] 3
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               39                33 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               39                33 
[1] "2p gain"
[1] 3
      2P GAIN CNV 2P GAIN WILD-TYPE 
                8                64 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                8                64 
[1] "2q gain"
[1] 3
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                65 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                65 
[1] "3p gain"
[1] 3
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3                69 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3                69 
[1] "3q gain"
[1] 3
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                69 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                69 
[1] "4p gain"
[1] 3
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6                66 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                6                66 
[1] "5p gain"
[1] 3
      5P GAIN CNV 5P GAIN WILD-TYPE 
               22                50 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               22                50 
[1] "5q gain"
[1] 3
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               16                56 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               16                56 
[1] "6p gain"
[1] 3
      6P GAIN CNV 6P GAIN WILD-TYPE 
               13                59 
      6P GAIN CNV 6P GAIN WILD-TYPE 
               13                59 
[1] "6q gain"
[1] 3
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                9                63 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                9                63 
[1] "7p gain"
[1] 3
      7P GAIN CNV 7P GAIN WILD-TYPE 
               18                54 
      7P GAIN CNV 7P GAIN WILD-TYPE 
               18                54 
[1] "7q gain"
[1] 3
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               19                53 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               19                53 
[1] "8p gain"
[1] 3
      8P GAIN CNV 8P GAIN WILD-TYPE 
               11                61 
      8P GAIN CNV 8P GAIN WILD-TYPE 
               11                61 
[1] "8q gain"
[1] 3
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               34                38 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               34                38 
[1] "9p gain"
[1] 3
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3                69 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                3                69 
[1] "9q gain"
[1] 3
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                69 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                3                69 
[1] "10p gain"
[1] 3
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                 66 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 6                 66 
[1] "12q gain"
[1] 3
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 3                 69 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 3                 69 
[1] "15q gain"
[1] 3
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                 67 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                 67 
[1] "16p gain"
[1] 3
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 69 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 69 
[1] "17p gain"
[1] 3
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                 69 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                 69 
[1] "17q gain"
[1] 3
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                17                 55 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                17                 55 
[1] "18p gain"
[1] 3
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 69 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 69 
[1] "18q gain"
[1] 3
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 68 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 68 
[1] "19p gain"
[1] 3
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 5                 67 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 5                 67 
[1] "19q gain"
[1] 3
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 7                 65 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 7                 65 
[1] "20p gain"
[1] 3
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 59 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                13                 59 
[1] "20q gain"
[1] 3
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                14                 58 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                14                 58 
[1] "21q gain"
[1] 3
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 4                 68 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 4                 68 
[1] "22q gain"
[1] 3
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 64 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 64 
[1] "Xq gain"
[1] 3
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4                68 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4                68 
[1] "1p loss"
[1] 3
      1P LOSS CNV 1P LOSS WILD-TYPE 
               13                59 
      1P LOSS CNV 1P LOSS WILD-TYPE 
               13                59 
[1] "1q loss"
[1] 3
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5                67 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5                67 
[1] "2p loss"
[1] 3
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                69 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                3                69 
[1] "2q loss"
[1] 3
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4                68 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                4                68 
[1] "3p loss"
[1] 3
      3P LOSS CNV 3P LOSS WILD-TYPE 
                7                65 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                7                65 
[1] "3q loss"
[1] 3
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                69 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                69 
[1] "4p loss"
[1] 3
      4P LOSS CNV 4P LOSS WILD-TYPE 
                9                63 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                9                63 
[1] "4q loss"
[1] 3
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               15                57 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               15                57 
[1] "5q loss"
[1] 3
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4                68 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4                68 
[1] "6q loss"
[1] 3
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12                60 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               12                60 
[1] "7p loss"
[1] 3
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5                67 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                5                67 
[1] "7q loss"
[1] 3
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                7                65 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                7                65 
[1] "8p loss"
[1] 3
      8P LOSS CNV 8P LOSS WILD-TYPE 
               30                42 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               30                42 
[1] "8q loss"
[1] 3
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                5                67 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                5                67 
[1] "9p loss"
[1] 3
      9P LOSS CNV 9P LOSS WILD-TYPE 
               17                55 
      9P LOSS CNV 9P LOSS WILD-TYPE 
               17                55 
[1] "9q loss"
[1] 3
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               15                57 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               15                57 
[1] "10p loss"
[1] 3
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 3                 69 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 3                 69 
[1] "10q loss"
[1] 3
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                13                 59 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                13                 59 
[1] "11p loss"
[1] 3
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 6                 66 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 6                 66 
[1] "11q loss"
[1] 3
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 8                 64 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 8                 64 
[1] "12p loss"
[1] 3
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 5                 67 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 5                 67 
[1] "12q loss"
[1] 3
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 3                 69 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 3                 69 
[1] "13q loss"
[1] 3
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                24                 48 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                24                 48 
[1] "14q loss"
[1] 3
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                24                 48 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                24                 48 
[1] "15q loss"
[1] 3
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 8                 64 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 8                 64 
[1] "16p loss"
[1] 3
      16P LOSS CNV 16P LOSS WILD-TYPE 
                15                 57 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                15                 57 
[1] "16q loss"
[1] 3
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                23                 49 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                23                 49 
[1] "17p loss"
[1] 3
      17P LOSS CNV 17P LOSS WILD-TYPE 
                30                 42 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                30                 42 
[1] "17q loss"
[1] 3
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 69 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 69 
[1] "18p loss"
[1] 3
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 8                 64 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 8                 64 
[1] "18q loss"
[1] 3
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                10                 62 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                10                 62 
[1] "19p loss"
[1] 3
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                 67 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                 67 
[1] "21q loss"
[1] 3
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                10                 62 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                10                 62 
[1] "22q loss"
[1] 3
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 9                 63 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 9                 63 
[1] "data2feature, selection="
 [1] "YEARSTOBIRTH"                     "DAYSTODEATH"                     
 [3] "DAYSTOLASTFOLLOWUP"               "VITALSTATUS"                     
 [5] "DCCUPLOADDATE"                    "PRIMARYSITEOFDESEASE"            
 [7] "GENDER"                           "DATEOFINITIALPATHOLOGICDIAGNOSIS"
 [9] "DAYSTOLASTKNOWNALIVE"             "HISTOLOGICALTYPE"                
[11] "DISTANT.METASTASIS"               "LYMPH.NODE.METASTASIS"           
[13] "COMPLETENESS.OF.RESECTION"        "TUMOR.STAGECODE"                 
[15] "NEOPLASM.DISEASESTAGE"            "BATCHNUMBER"                     

Input Data has 16 rows and 72 columns.

[1] "Batch" "16"   
[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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
           2            3            4         1678           NA           NA 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
          NA          693           NA           79           NA          652 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
          NA           NA         2414         2017          601         1628 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
         203         1036          183          887           NA          129 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
         110          111           60           NA           97           13 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A3R3 TCGA-G3-A25S 
          NA           NA           NA           NA            4           37 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1175         1231          434          390         1359           NA 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
         269          253          192          179          136           27 
Variable 1:'AGE':	nDistinctValues=38,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'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=15,	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:'DISTANT.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'LYMPH.NODE.METASTASIS':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'TUMOR.STAGECODE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'BATCH.NUMBER':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"                       "GENDER"                   
[3] "DISTANT.METASTASIS"        "LYMPH.NODE.METASTASIS"    
[5] "COMPLETENESS.OF.RESECTION" "TUMOR.STAGECODE"          
[7] "NEOPLASM.DISEASESTAGE"    
[1] "TUMOR.?STAGE" "6"           
[1] "stage2"
vv
 T1  T2  T3 T3A T3B  T4 
 32  13  12   8   2   5 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 72 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=38, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
DISTANT.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
LYMPH.NODE.METASTASIS, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
TUMOR.STAGECODE, nv=0, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1p gain
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN CNV        4  3
  1P GAIN WILD-TYPE 36 23
      1P GAIN CNV 1P GAIN WILD-TYPE 
                7                59 
      1P GAIN CNV 1P GAIN WILD-TYPE 
                3                23 
$`1P GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        8.28         0.07         4.24         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       55.17        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-A1EA 
        2.60         0.46        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL 
       29.16        13.64         3.65         1.97         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        0.43        22.85        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      1P GAIN CNV 1P GAIN WILD-TYPE 
             2.99              0.07 
      1P GAIN CNV 1P GAIN WILD-TYPE 
            37.61             90.67 
      1P GAIN CNV 1P GAIN WILD-TYPE 
            12.82             13.64 
[1] "3.0 - 37.6 (12.8)" "0.1 - 90.7 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV" "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 CNV"       "1P GAIN CNV" 
       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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" "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 CNV" "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 CNV"       "1P GAIN CNV" 
       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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" "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 CNV" "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 CNV"       "1P GAIN CNV" 
       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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"       "1P GAIN CNV"       "1P GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D1V2, continuous
D1V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN CNV          3    5
  1P GAIN WILD-TYPE   22   42
        clus
vv       1P GAIN CNV 1P GAIN WILD-TYPE
  FEMALE           3                22
  MALE             5                42
                   vv
clus                M0 M1 MX
  1P GAIN CNV        3  0  5
  1P GAIN WILD-TYPE 45  1 18
D1V4, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  M0           3                45
  M1           0                 1
  MX           5                18
                   vv
clus                N0 N1 NX
  1P GAIN CNV        3  0  5
  1P GAIN WILD-TYPE 46  1 16
D1V5, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  N0           3                46
  N1           0                 1
  NX           5                16
                   vv
clus                R0 R1 R2 RX
  1P GAIN CNV        3  3  0  0
  1P GAIN WILD-TYPE 47  5  1  8
D1V6, multiclass
    clus
vv   1P GAIN CNV 1P GAIN WILD-TYPE
  R0           3                47
  R1           3                 5
  R2           0                 1
  RX           0                 8
D1V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1P GAIN CNV             2        0          1          2          0         0
  1P GAIN WILD-TYPE      27       12         15          2          1         1
D1V8, multiclass

Clustering(2) Variable = 1q gain
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN CNV       23 12
  1Q GAIN WILD-TYPE 17 14
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               35                31 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
               12                14 
$`1Q GAIN CNV`
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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
       37.61         8.28         0.07         0.13        55.17        37.74 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE 
       22.78         7.33        21.44        90.67        79.36         6.67 
TCGA-DD-A1EH TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       34.06        13.64         4.24         3.62         3.65         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25W 
        0.62         3.19        19.07         0.13         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-CC-A3MB 
       69.57        13.81         0.26         0.07         4.24         0.10 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EB 
       83.57        53.29         2.60         0.46        51.25        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A3RK TCGA-ES-A2HS 
       19.76        53.52         6.02        29.16         0.43        22.85 
TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH 
       14.40        38.63        40.47        14.27        14.86         6.31 
TCGA-G3-A3CI 
        5.88 

      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             0.07              0.07 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
            90.67             83.57 
      1Q GAIN CNV 1Q GAIN WILD-TYPE 
             8.32             14.86 
[1] "0.1 - 90.7 (8.3)"  "0.1 - 83.6 (14.9)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
      "1Q GAIN CNV"       "1Q GAIN CNV" "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 CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
      "1Q GAIN CNV"       "1Q GAIN CNV" "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 CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"1Q GAIN WILD-TYPE"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV"       "1Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"       "1Q GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
      "1Q GAIN CNV"       "1Q GAIN CNV" "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 CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "1Q GAIN CNV"       "1Q GAIN CNV" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "1Q GAIN CNV"       "1Q GAIN CNV" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN CNV         11   28
  1Q GAIN WILD-TYPE   14   19
        clus
vv       1Q GAIN CNV 1Q GAIN WILD-TYPE
  FEMALE          11                14
  MALE            28                19
                   vv
clus                M0 M1 MX
  1Q GAIN CNV       24  1 14
  1Q GAIN WILD-TYPE 24  0  9
D2V4, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  M0          24                24
  M1           1                 0
  MX          14                 9
                   vv
clus                N0 N1 NX
  1Q GAIN CNV       25  0 13
  1Q GAIN WILD-TYPE 24  1  8
D2V5, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  N0          25                24
  N1           0                 1
  NX          13                 8
                   vv
clus                R0 R1 R2 RX
  1Q GAIN CNV       26  5  1  4
  1Q GAIN WILD-TYPE 24  3  0  4
D2V6, multiclass
    clus
vv   1Q GAIN CNV 1Q GAIN WILD-TYPE
  R0          26                24
  R1           5                 3
  R2           1                 0
  RX           4                 4
D2V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1Q GAIN CNV            14        9          6          3          0         1
  1Q GAIN WILD-TYPE      15        3         10          1          1         0
D2V8, multiclass

Clustering(3) Variable = 2p gain
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN CNV        3  5
  2P GAIN WILD-TYPE 37 21
      2P GAIN CNV 2P GAIN WILD-TYPE 
                8                58 
      2P GAIN CNV 2P GAIN WILD-TYPE 
                5                21 
$`2P GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
        8.28         0.07         4.24         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       55.17        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-A1EA 
        2.60         0.46        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       29.16        13.64         4.24         3.62         3.65         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62         3.19         0.43        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      2P GAIN CNV 2P GAIN WILD-TYPE 
             8.84              0.07 
      2P GAIN CNV 2P GAIN WILD-TYPE 
            48.99             90.67 
      2P GAIN CNV 2P GAIN WILD-TYPE 
           25.185             9.945 
[1] "8.8 - 49.0 (25.2)" "0.1 - 90.7 (9.9)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2P GAIN CNV" "2P GAIN WILD-TYPE"       "2P GAIN CNV"       "2P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "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-CC-A3MA 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"       "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2P GAIN CNV" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN CNV          5    3
  2P GAIN WILD-TYPE   20   44
        clus
vv       2P GAIN CNV 2P GAIN WILD-TYPE
  FEMALE           5                20
  MALE             3                44
                   vv
clus                M0 M1 MX
  2P GAIN CNV        4  0  4
  2P GAIN WILD-TYPE 44  1 19
D3V4, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  M0           4                44
  M1           0                 1
  MX           4                19
                   vv
clus                N0 N1 NX
  2P GAIN CNV        4  0  4
  2P GAIN WILD-TYPE 45  1 17
D3V5, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  N0           4                45
  N1           0                 1
  NX           4                17
                   vv
clus                R0 R1 R2 RX
  2P GAIN CNV        5  3  0  0
  2P GAIN WILD-TYPE 45  5  1  8
D3V6, multiclass
    clus
vv   2P GAIN CNV 2P GAIN WILD-TYPE
  R0           5                45
  R1           3                 5
  R2           0                 1
  RX           0                 8
D3V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2P GAIN CNV             2        1          1          1          0         0
  2P GAIN WILD-TYPE      27       11         15          3          1         1
D3V8, multiclass

Clustering(4) Variable = 2q gain
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN CNV        3  4
  2Q GAIN WILD-TYPE 37 22
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                7                59 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
                4                22 
$`2Q GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB 
        0.26         8.28         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
        1.97         0.62         3.19         0.43        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
        0.13         1.22        40.47        14.27        44.68        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      2Q GAIN CNV 2Q GAIN WILD-TYPE 
             8.84              0.07 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
            48.99             90.67 
      2Q GAIN CNV 2Q GAIN WILD-TYPE 
            22.85             11.57 
[1] "8.8 - 49.0 (22.9)" "0.1 - 90.7 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       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-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       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-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV"       "2Q GAIN CNV" 
       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-CC-A3MA 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"       "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "2Q GAIN CNV" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D4V2, continuous
D4V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN CNV          5    2
  2Q GAIN WILD-TYPE   20   45
        clus
vv       2Q GAIN CNV 2Q GAIN WILD-TYPE
  FEMALE           5                20
  MALE             2                45
                   vv
clus                M0 M1 MX
  2Q GAIN CNV        4  0  3
  2Q GAIN WILD-TYPE 44  1 20
D4V4, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  M0           4                44
  M1           0                 1
  MX           3                20
                   vv
clus                N0 N1 NX
  2Q GAIN CNV        4  0  3
  2Q GAIN WILD-TYPE 45  1 18
D4V5, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  N0           4                45
  N1           0                 1
  NX           3                18
                   vv
clus                R0 R1 R2 RX
  2Q GAIN CNV        5  2  0  0
  2Q GAIN WILD-TYPE 45  6  1  8
D4V6, multiclass
    clus
vv   2Q GAIN CNV 2Q GAIN WILD-TYPE
  R0           5                45
  R1           2                 6
  R2           0                 1
  RX           0                 8
D4V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2Q GAIN CNV             2        1          1          1          0         0
  2Q GAIN WILD-TYPE      27       11         15          3          1         1
D4V8, multiclass

Clustering(5) Variable = 3p gain
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN CNV        2  1
  3P GAIN WILD-TYPE 38 25
      3P GAIN CNV 3P GAIN WILD-TYPE 
                3                63 
      3P GAIN CNV 3P GAIN WILD-TYPE 
                1                25 
$`3P GAIN CNV`
TCGA-DD-A11C TCGA-DD-A1EJ TCGA-ES-A2HS 
       21.44        29.16        22.85 

$`3P 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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.07         0.10         0.13        55.17        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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
        6.67        34.06         6.02        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      3P GAIN CNV 3P GAIN WILD-TYPE 
            21.44              0.07 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            29.16             90.67 
      3P GAIN CNV 3P GAIN WILD-TYPE 
            22.85             11.57 
[1] "21.4 - 29.2 (22.9)" "0.1 - 90.7 (11.6)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P GAIN WILD-TYPE"       "3P GAIN CNV" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D5V2, continuous
D5V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN CNV          1    2
  3P GAIN WILD-TYPE   24   45
        clus
vv       3P GAIN CNV 3P GAIN WILD-TYPE
  FEMALE           1                24
  MALE             2                45
                   vv
clus                M0 M1 MX
  3P GAIN CNV        2  0  1
  3P GAIN WILD-TYPE 46  1 22
D5V4, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  3P GAIN CNV        1  1  1
  3P GAIN WILD-TYPE 48  0 20
D5V5, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  N0           1                48
  N1           1                 0
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  3P GAIN CNV        2  0  0  1
  3P GAIN WILD-TYPE 48  8  1  7
D5V6, multiclass
    clus
vv   3P GAIN CNV 3P GAIN WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           1                 7
D5V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3P GAIN CNV             2        0          0          0          1         0
  3P GAIN WILD-TYPE      27       12         16          4          0         1
D5V8, multiclass

Clustering(6) Variable = 3q gain
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN CNV        2  1
  3Q GAIN WILD-TYPE 38 25
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                3                63 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
                1                25 
$`3Q GAIN CNV`
TCGA-DD-A11C TCGA-DD-A1EJ TCGA-ES-A2HS 
       21.44        29.16        22.85 

$`3Q 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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.07         0.10         0.13        55.17        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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
        6.67        34.06         6.02        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            21.44              0.07 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            29.16             90.67 
      3Q GAIN CNV 3Q GAIN WILD-TYPE 
            22.85             11.57 
[1] "21.4 - 29.2 (22.9)" "0.1 - 90.7 (11.6)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q GAIN WILD-TYPE"       "3Q GAIN CNV" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D6V2, continuous
D6V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN CNV          1    2
  3Q GAIN WILD-TYPE   24   45
        clus
vv       3Q GAIN CNV 3Q GAIN WILD-TYPE
  FEMALE           1                24
  MALE             2                45
                   vv
clus                M0 M1 MX
  3Q GAIN CNV        2  0  1
  3Q GAIN WILD-TYPE 46  1 22
D6V4, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  3Q GAIN CNV        1  1  1
  3Q GAIN WILD-TYPE 48  0 20
D6V5, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  N0           1                48
  N1           1                 0
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  3Q GAIN CNV        2  0  0  1
  3Q GAIN WILD-TYPE 48  8  1  7
D6V6, multiclass
    clus
vv   3Q GAIN CNV 3Q GAIN WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           1                 7
D6V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3Q GAIN CNV             2        0          0          0          1         0
  3Q GAIN WILD-TYPE      27       12         16          4          0         1
D6V8, multiclass

Clustering(7) Variable = 4p gain
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN CNV        4  1
  4P GAIN WILD-TYPE 36 25
      4P GAIN CNV 4P GAIN WILD-TYPE 
                5                61 
      4P GAIN CNV 4P GAIN WILD-TYPE 
                1                25 
$`4P GAIN CNV`
TCGA-BC-A10R TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EH 
       10.13         0.10        22.78        19.76        34.06 

$`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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        55.17        37.74        83.57        53.29 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EJ 
       79.36        66.31        53.52         6.67         6.02        29.16 
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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        3.19         0.43        22.85        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      4P GAIN CNV 4P GAIN WILD-TYPE 
             0.10              0.07 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            34.06             90.67 
      4P GAIN CNV 4P GAIN WILD-TYPE 
            19.76             12.82 
[1] "0.1 - 34.1 (19.8)" "0.1 - 90.7 (12.8)"
       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 CNV" 
       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-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" "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 CNV" 
       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-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" "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 CNV" 
       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-CC-A3MA 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "4P GAIN CNV" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"       "4P GAIN CNV" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
[1] "hr=" "1.3"
D7V2, continuous
D7V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN CNV          3    3
  4P GAIN WILD-TYPE   22   44
        clus
vv       4P GAIN CNV 4P GAIN WILD-TYPE
  FEMALE           3                22
  MALE             3                44
                   vv
clus                M0 M1 MX
  4P GAIN CNV        5  0  1
  4P GAIN WILD-TYPE 43  1 22
D7V4, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  M0           5                43
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  4P GAIN CNV        5  0  1
  4P GAIN WILD-TYPE 44  1 20
D7V5, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  N0           5                44
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  4P GAIN CNV        5  0  0  1
  4P GAIN WILD-TYPE 45  8  1  7
D7V6, multiclass
    clus
vv   4P GAIN CNV 4P GAIN WILD-TYPE
  R0           5                45
  R1           0                 8
  R2           0                 1
  RX           1                 7
D7V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  4P GAIN CNV             2        1          1          1          0         0
  4P GAIN WILD-TYPE      27       11         15          3          1         1
D7V8, multiclass

Clustering(8) Variable = 5p gain
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN CNV       11 10
  5P GAIN WILD-TYPE 29 16
      5P GAIN CNV 5P GAIN WILD-TYPE 
               21                45 
      5P GAIN CNV 5P GAIN WILD-TYPE 
               10                16 
$`5P GAIN CNV`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KG TCGA-CC-5263 TCGA-CC-A3MB 
       37.32         2.99         5.03         8.28         4.24         0.10 
TCGA-CC-A3MC TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 
        0.13        83.57        53.29        22.78        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR 
       79.36        66.31         1.97         3.19        14.40        19.07 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG 
       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-CC-A3MA TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 
        0.26         0.07         0.07        55.17        37.74         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
        2.60         0.46        21.44        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-FV-A3R3 TCGA-G3-A25S 
        3.65         0.62         0.43        22.85         0.13         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       38.63        40.47        14.27        14.86         8.84         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      5P GAIN CNV 5P GAIN WILD-TYPE 
             0.10              0.07 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            90.67             69.57 
      5P GAIN CNV 5P GAIN WILD-TYPE 
            14.40             11.57 
[1] "0.1 - 90.7 (14.4)" "0.1 - 69.6 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "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 CNV" 
       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 CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P GAIN WILD-TYPE" "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 CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" "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 CNV" "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 CNV" 
       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 CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P GAIN WILD-TYPE" "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 CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" "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 CNV" "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 CNV" 
       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 CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5P GAIN CNV"       "5P GAIN CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE"       "5P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"       "5P GAIN CNV"       "5P GAIN CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5P GAIN WILD-TYPE" "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 CNV"       "5P GAIN CNV" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"       "5P GAIN CNV" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D8V2, continuous
D8V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN CNV          7   15
  5P GAIN WILD-TYPE   18   32
        clus
vv       5P GAIN CNV 5P GAIN WILD-TYPE
  FEMALE           7                18
  MALE            15                32
                   vv
clus                M0 M1 MX
  5P GAIN CNV       16  0  6
  5P GAIN WILD-TYPE 32  1 17
D8V4, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  M0          16                32
  M1           0                 1
  MX           6                17
                   vv
clus                N0 N1 NX
  5P GAIN CNV       16  0  6
  5P GAIN WILD-TYPE 33  1 15
D8V5, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  N0          16                33
  N1           0                 1
  NX           6                15
                   vv
clus                R0 R1 R2 RX
  5P GAIN CNV       15  3  0  3
  5P GAIN WILD-TYPE 35  5  1  5
D8V6, multiclass
    clus
vv   5P GAIN CNV 5P GAIN WILD-TYPE
  R0          15                35
  R1           3                 5
  R2           0                 1
  RX           3                 5
D8V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  5P GAIN CNV             9        3          6          1          0         0
  5P GAIN WILD-TYPE      20        9         10          3          1         1
D8V8, multiclass

Clustering(9) Variable = 5q gain
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN CNV        7  8
  5Q GAIN WILD-TYPE 33 18
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
               15                51 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
                8                18 
$`5Q GAIN CNV`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
       37.32         2.99         5.03         0.10         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-EP-A2KB 
       53.29        22.78        51.25        90.67        79.36         1.97 
TCGA-ES-A2HT TCGA-G3-A25W TCGA-G3-A3CG 
       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-CC-A3MA TCGA-DD-A113 
        0.26         8.28         0.07         4.24         0.07        55.17 
TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB 
       37.74         7.33         2.60         0.46        21.44        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.76        53.52         6.67        34.06         6.02        29.16 
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-EP-A3RK TCGA-ES-A2HS TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T 
        0.43        22.85        19.07         0.13         1.22        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       40.47        14.27        44.68        14.86         8.84         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      5Q GAIN CNV 5Q GAIN WILD-TYPE 
             0.10              0.07 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            90.67             69.57 
      5Q GAIN CNV 5Q GAIN WILD-TYPE 
            14.40             11.57 
[1] "0.1 - 90.7 (14.4)" "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 CNV" "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 CNV" 
       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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5Q GAIN CNV"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" "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 CNV" "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 CNV" 
       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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5Q GAIN CNV"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" "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 CNV" "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 CNV" 
       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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "5Q GAIN CNV"       "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "5Q GAIN CNV"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"       "5Q GAIN CNV" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D9V2, continuous
D9V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN CNV          5   11
  5Q GAIN WILD-TYPE   20   36
        clus
vv       5Q GAIN CNV 5Q GAIN WILD-TYPE
  FEMALE           5                20
  MALE            11                36
                   vv
clus                M0 M1 MX
  5Q GAIN CNV       11  0  5
  5Q GAIN WILD-TYPE 37  1 18
D9V4, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  M0          11                37
  M1           0                 1
  MX           5                18
                   vv
clus                N0 N1 NX
  5Q GAIN CNV       11  0  5
  5Q GAIN WILD-TYPE 38  1 16
D9V5, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  N0          11                38
  N1           0                 1
  NX           5                16
                   vv
clus                R0 R1 R2 RX
  5Q GAIN CNV       12  3  0  1
  5Q GAIN WILD-TYPE 38  5  1  7
D9V6, multiclass
    clus
vv   5Q GAIN CNV 5Q GAIN WILD-TYPE
  R0          12                38
  R1           3                 5
  R2           0                 1
  RX           1                 7
D9V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  5Q GAIN CNV             6        1          5          1          0         0
  5Q GAIN WILD-TYPE      23       11         11          3          1         1
D9V8, multiclass

Clustering(10) Variable = 6p gain
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN CNV        7  5
  6P GAIN WILD-TYPE 33 21
      6P GAIN CNV 6P GAIN WILD-TYPE 
               12                54 
      6P GAIN CNV 6P GAIN WILD-TYPE 
                5                21 
$`6P GAIN CNV`
TCGA-BC-A10U TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A119 TCGA-DD-A1EH 
       27.52         0.26         8.28         4.24         7.33        34.06 
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-BC-A217 TCGA-CC-5258 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC 
       37.61        13.81         0.07         0.07         0.10         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
       55.17        37.74        83.57        53.29        22.78         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.44        51.25        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       19.76        53.52         6.67         6.02        29.16        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        4.24         3.62         3.65         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        38.63        40.47        14.27        12.82 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         6.31         5.88         4.47         0.89 

      6P GAIN CNV 6P GAIN WILD-TYPE 
             0.26              0.07 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            44.68             90.67 
      6P GAIN CNV 6P GAIN WILD-TYPE 
            7.805            14.040 
[1] "0.3 - 44.7 (7.8)"  "0.1 - 90.7 (14.0)"
       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 CNV" "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 WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "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 CNV" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" "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 CNV" "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 WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "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 CNV" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" "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 CNV" "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 WILD-TYPE"       "6P GAIN CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "6P GAIN CNV" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6P GAIN WILD-TYPE"       "6P GAIN CNV"       "6P GAIN CNV" "6P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "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 CNV" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"       "6P GAIN CNV" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D10V2, continuous
D10V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN CNV          3   10
  6P GAIN WILD-TYPE   22   37
        clus
vv       6P GAIN CNV 6P GAIN WILD-TYPE
  FEMALE           3                22
  MALE            10                37
                   vv
clus                M0 M1 MX
  6P GAIN CNV        8  1  4
  6P GAIN WILD-TYPE 40  0 19
D10V4, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  M0           8                40
  M1           1                 0
  MX           4                19
                   vv
clus                N0 N1 NX
  6P GAIN CNV        8  0  5
  6P GAIN WILD-TYPE 41  1 16
D10V5, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  N0           8                41
  N1           0                 1
  NX           5                16
                   vv
clus                R0 R1 R2 RX
  6P GAIN CNV        7  3  1  2
  6P GAIN WILD-TYPE 43  5  0  6
D10V6, multiclass
    clus
vv   6P GAIN CNV 6P GAIN WILD-TYPE
  R0           7                43
  R1           3                 5
  R2           1                 0
  RX           2                 6
D10V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  6P GAIN CNV             6        2          2          1          0         1
  6P GAIN WILD-TYPE      23       10         14          3          1         0
D10V8, multiclass

Clustering(11) Variable = 6q gain
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN CNV        5  3
  6Q GAIN WILD-TYPE 35 23
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                8                58 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
                3                23 
$`6Q GAIN CNV`
TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A119 TCGA-DD-A1EH TCGA-EP-A2KB TCGA-EP-A2KC 
        8.28         4.24         7.33        34.06         1.97         0.62 
TCGA-G3-A25S TCGA-G3-A3CG 
        1.22         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-CC-A3MA 
        5.03        37.61        13.81         0.26         0.07         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI 
       79.36        66.31        19.76        53.52         6.67         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
       29.16        13.64         4.24         3.62         3.65         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         0.13        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      6Q GAIN CNV 6Q GAIN WILD-TYPE 
             0.62              0.07 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            34.06             90.67 
      6Q GAIN CNV 6Q GAIN WILD-TYPE 
            5.785            14.335 
[1] "0.6 - 34.1 (5.8)"  "0.1 - 90.7 (14.3)"
       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-CC-A3MA 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" "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-CC-A3MA 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" "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-CC-A3MA 
      "6Q GAIN CNV" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"       "6Q GAIN CNV" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
[1] "hr=" "3"  
D11V2, continuous
D11V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN CNV          2    7
  6Q GAIN WILD-TYPE   23   40
        clus
vv       6Q GAIN CNV 6Q GAIN WILD-TYPE
  FEMALE           2                23
  MALE             7                40
                   vv
clus                M0 M1 MX
  6Q GAIN CNV        6  1  2
  6Q GAIN WILD-TYPE 42  0 21
D11V4, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  M0           6                42
  M1           1                 0
  MX           2                21
                   vv
clus                N0 N1 NX
  6Q GAIN CNV        7  0  2
  6Q GAIN WILD-TYPE 42  1 19
D11V5, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  N0           7                42
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  6Q GAIN CNV        4  2  1  2
  6Q GAIN WILD-TYPE 46  6  0  6
D11V6, multiclass
    clus
vv   6Q GAIN CNV 6Q GAIN WILD-TYPE
  R0           4                46
  R1           2                 6
  R2           1                 0
  RX           2                 6
D11V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  6Q GAIN CNV             4        1          2          1          0         1
  6Q GAIN WILD-TYPE      25       11         14          3          1         0
D11V8, multiclass

Clustering(12) Variable = 7p gain
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN CNV       10  6
  7P GAIN WILD-TYPE 30 20
      7P GAIN CNV 7P GAIN WILD-TYPE 
               16                50 
      7P GAIN CNV 7P GAIN WILD-TYPE 
                6                20 
$`7P GAIN CNV`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 
       37.32        10.13        27.52         0.10        55.17        22.78 
TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1EC TCGA-DD-A1EE TCGA-EP-A2KC TCGA-EP-A3JL 
        2.60        51.25        19.76         6.67         0.62         3.19 
TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
       22.85        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-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MC 
        0.26         8.28         0.07         4.24         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C 
       37.74        83.57        53.29         7.33         0.46        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI 
       90.67        79.36        66.31        53.52        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
       29.16        13.64         4.24         3.62         3.65         1.97 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U 
        0.43        14.40        19.07         0.13         1.22        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
       14.27        12.82        44.68        14.86         8.84         6.31 
TCGA-G3-A3CI TCGA-G3-A3CK 
        5.88         0.89 

      7P GAIN CNV 7P GAIN WILD-TYPE 
             0.10              0.07 
      7P GAIN CNV 7P GAIN WILD-TYPE 
            55.17             90.67 
      7P GAIN CNV 7P GAIN WILD-TYPE 
           14.945            13.230 
[1] "0.1 - 55.2 (14.9)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7P GAIN CNV" "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 CNV"       "7P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7P GAIN CNV" "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 CNV"       "7P GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7P GAIN CNV" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV"       "7P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"       "7P GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"       "7P GAIN CNV" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7P GAIN CNV" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN CNV          8   10
  7P GAIN WILD-TYPE   17   37
        clus
vv       7P GAIN CNV 7P GAIN WILD-TYPE
  FEMALE           8                17
  MALE            10                37
                   vv
clus                M0 M1 MX
  7P GAIN CNV       12  0  6
  7P GAIN WILD-TYPE 36  1 17
D12V4, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  M0          12                36
  M1           0                 1
  MX           6                17
                   vv
clus                N0 N1 NX
  7P GAIN CNV       12  0  6
  7P GAIN WILD-TYPE 37  1 15
D12V5, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  N0          12                37
  N1           0                 1
  NX           6                15
                   vv
clus                R0 R1 R2 RX
  7P GAIN CNV       12  3  0  2
  7P GAIN WILD-TYPE 38  5  1  6
D12V6, multiclass
    clus
vv   7P GAIN CNV 7P GAIN WILD-TYPE
  R0          12                38
  R1           3                 5
  R2           0                 1
  RX           2                 6
D12V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7P GAIN CNV             8        3          3          1          0         0
  7P GAIN WILD-TYPE      21        9         13          3          1         1
D12V8, multiclass

Clustering(13) Variable = 7q gain
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN CNV       11  6
  7Q GAIN WILD-TYPE 29 20
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
               17                49 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
                6                20 
$`7Q GAIN CNV`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11A 
       37.32        10.13        27.52         0.10        22.78         2.60 
TCGA-DD-A11D TCGA-DD-A1EC TCGA-DD-A1EE TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       51.25        19.76         6.67         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
        3.19        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-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MC 
        0.26         8.28         0.07         4.24         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B 
       55.17        37.74        83.57        53.29         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH 
       21.44        90.67        79.36        66.31        53.52        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK 
        6.02        29.16        13.64         4.24         1.97         0.43 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         0.13         1.22        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       12.82        44.68        14.86         8.84         6.31         5.88 
TCGA-G3-A3CK 
        0.89 

      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             0.10              0.07 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
            51.25             90.67 
      7Q GAIN CNV 7Q GAIN WILD-TYPE 
             8.32             13.81 
[1] "0.1 - 51.2 (8.3)"  "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 CNV"       "7Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7Q GAIN CNV" "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 CNV"       "7Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7Q GAIN CNV" "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 CNV"       "7Q GAIN CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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 WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV"       "7Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"       "7Q GAIN CNV" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "7Q GAIN CNV" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN CNV          8   11
  7Q GAIN WILD-TYPE   17   36
        clus
vv       7Q GAIN CNV 7Q GAIN WILD-TYPE
  FEMALE           8                17
  MALE            11                36
                   vv
clus                M0 M1 MX
  7Q GAIN CNV       11  0  8
  7Q GAIN WILD-TYPE 37  1 15
D13V4, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  M0          11                37
  M1           0                 1
  MX           8                15
                   vv
clus                N0 N1 NX
  7Q GAIN CNV       12  0  7
  7Q GAIN WILD-TYPE 37  1 14
D13V5, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  N0          12                37
  N1           0                 1
  NX           7                14
                   vv
clus                R0 R1 R2 RX
  7Q GAIN CNV       12  3  0  2
  7Q GAIN WILD-TYPE 38  5  1  6
D13V6, multiclass
    clus
vv   7Q GAIN CNV 7Q GAIN WILD-TYPE
  R0          12                38
  R1           3                 5
  R2           0                 1
  RX           2                 6
D13V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7Q GAIN CNV             9        2          4          1          0         0
  7Q GAIN WILD-TYPE      20       10         12          3          1         1
D13V8, multiclass

Clustering(14) Variable = 8p gain
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN CNV        7  3
  8P GAIN WILD-TYPE 33 23
      8P GAIN CNV 8P GAIN WILD-TYPE 
               10                56 
      8P GAIN CNV 8P GAIN WILD-TYPE 
                3                23 
$`8P GAIN CNV`
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-CC-A3MA 
       37.61        13.81         0.26         8.28         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB 
       22.78         0.46        21.44        51.25        79.36        66.31 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       14.40        19.07         0.13         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       14.27        12.82        14.86         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      8P GAIN CNV 8P GAIN WILD-TYPE 
             0.07              0.07 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            90.67             83.57 
      8P GAIN CNV 8P GAIN WILD-TYPE 
            8.085            13.725 
[1] "0.1 - 90.7 (8.1)"  "0.1 - 83.6 (13.7)"
       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 CNV" "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-CC-A3MA 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" "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 CNV" "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-CC-A3MA 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" "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 CNV" "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-CC-A3MA 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8P GAIN WILD-TYPE"       "8P GAIN CNV" "8P GAIN WILD-TYPE"       "8P GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8P GAIN CNV" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D14V2, continuous
D14V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN CNV          2    9
  8P GAIN WILD-TYPE   23   38
        clus
vv       8P GAIN CNV 8P GAIN WILD-TYPE
  FEMALE           2                23
  MALE             9                38
                   vv
clus                M0 M1 MX
  8P GAIN CNV        7  1  3
  8P GAIN WILD-TYPE 41  0 20
D14V4, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  M0           7                41
  M1           1                 0
  MX           3                20
                   vv
clus                N0 N1 NX
  8P GAIN CNV        8  0  3
  8P GAIN WILD-TYPE 41  1 18
D14V5, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  N0           8                41
  N1           0                 1
  NX           3                18
                   vv
clus                R0 R1 R2 RX
  8P GAIN CNV        7  0  1  2
  8P GAIN WILD-TYPE 43  8  0  6
D14V6, multiclass
    clus
vv   8P GAIN CNV 8P GAIN WILD-TYPE
  R0           7                43
  R1           0                 8
  R2           1                 0
  RX           2                 6
D14V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8P GAIN CNV             6        2          1          0          0         1
  8P GAIN WILD-TYPE      23       10         15          4          1         0
D14V8, multiclass

Clustering(15) Variable = 8q gain
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN CNV       21 10
  8Q GAIN WILD-TYPE 19 16
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               31                35 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
               10                16 
$`8Q GAIN CNV`
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-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
        0.13        55.17        53.29        22.78         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EI TCGA-EP-A12J 
       21.44        90.67        19.76         6.67         6.02         4.24 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.65         1.97         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       14.40        38.63        12.82        44.68         8.84         8.32 
TCGA-G3-A3CJ 
        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-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
        4.24         0.07         0.10        37.74        83.57         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ 
       51.25        79.36        66.31        53.52        34.06        29.16 
TCGA-DD-A1EL TCGA-EP-A26S TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U 
       13.64         3.62        19.07         0.13         1.22        40.47 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.27        14.86         6.31         5.88         0.89 

      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             0.07              0.07 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
            90.67             83.57 
      8Q GAIN CNV 8Q GAIN WILD-TYPE 
             8.32             14.27 
[1] "0.1 - 90.7 (8.3)"  "0.1 - 83.6 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8Q GAIN CNV" "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 CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8Q GAIN CNV" "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 CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8Q GAIN CNV" "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 CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8Q GAIN CNV"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"       "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "8Q GAIN CNV"       "8Q GAIN CNV" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8Q GAIN CNV" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN CNV         10   24
  8Q GAIN WILD-TYPE   15   23
        clus
vv       8Q GAIN CNV 8Q GAIN WILD-TYPE
  FEMALE          10                15
  MALE            24                23
                   vv
clus                M0 M1 MX
  8Q GAIN CNV       21  1 12
  8Q GAIN WILD-TYPE 27  0 11
D15V4, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  M0          21                27
  M1           1                 0
  MX          12                11
                   vv
clus                N0 N1 NX
  8Q GAIN CNV       22  0 12
  8Q GAIN WILD-TYPE 27  1  9
D15V5, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  N0          22                27
  N1           0                 1
  NX          12                 9
                   vv
clus                R0 R1 R2 RX
  8Q GAIN CNV       23  4  1  3
  8Q GAIN WILD-TYPE 27  4  0  5
D15V6, multiclass
    clus
vv   8Q GAIN CNV 8Q GAIN WILD-TYPE
  R0          23                27
  R1           4                 4
  R2           1                 0
  RX           3                 5
D15V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8Q GAIN CNV            15        6          8          1          0         1
  8Q GAIN WILD-TYPE      14        6          8          3          1         0
D15V8, multiclass

Clustering(16) Variable = 9p gain
D16V1, survival
                   sevent
clus2                0  1
  9P GAIN CNV        2  0
  9P GAIN WILD-TYPE 38 26
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2                64 
      9P GAIN CNV 9P GAIN WILD-TYPE 
                0                26 
$`9P GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        4.24         3.62         3.65         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T 
       22.85        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      9P GAIN CNV 9P GAIN WILD-TYPE 
             1.97              0.07 
      9P GAIN CNV 9P GAIN WILD-TYPE 
            40.47             90.67 
      9P GAIN CNV 9P GAIN WILD-TYPE 
            21.22             13.23 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (13.2)"
       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-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" "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-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" "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-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P GAIN WILD-TYPE"       "9P GAIN CNV" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"       "9P GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9P GAIN CNV"           
clus
      9P GAIN CNV 9P GAIN WILD-TYPE 
                2                64 
       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-CC-A3MA 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3R3 
"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-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
D16V2, continuous
D16V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN CNV          2    1
  9P GAIN WILD-TYPE   23   46
        clus
vv       9P GAIN CNV 9P GAIN WILD-TYPE
  FEMALE           2                23
  MALE             1                46
                   vv
clus                M0 M1 MX
  9P GAIN CNV        2  0  1
  9P GAIN WILD-TYPE 46  1 22
D16V4, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  9P GAIN CNV        2  0  1
  9P GAIN WILD-TYPE 47  1 20
D16V5, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  9P GAIN CNV        2  0  0  1
  9P GAIN WILD-TYPE 48  8  1  7
D16V6, multiclass
    clus
vv   9P GAIN CNV 9P GAIN WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           1                 7
D16V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9P GAIN CNV             2        0          1          0          0         0
  9P GAIN WILD-TYPE      27       12         15          4          1         1
D16V8, multiclass

Clustering(17) Variable = 9q gain
D17V1, survival
                   sevent
clus2                0  1
  9Q GAIN CNV        2  0
  9Q GAIN WILD-TYPE 38 26
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                2                64 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                0                26 
$`9Q GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 
        4.24         0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        13.64 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        4.24         3.62         3.65         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T 
       22.85        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      9Q GAIN CNV 9Q GAIN WILD-TYPE 
             1.97              0.07 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
            40.47             90.67 
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
            21.22             13.23 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (13.2)"
       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-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" "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-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" "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-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q GAIN WILD-TYPE"       "9Q GAIN CNV" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3RK        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-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"       "9Q GAIN CNV" 
       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-A3CH        TCGA-G3-A3CI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "9Q GAIN CNV"           
clus
      9Q GAIN CNV 9Q GAIN WILD-TYPE 
                2                64 
       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-CC-A3MA 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3R3 
"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-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
D17V2, continuous
D17V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN CNV          2    1
  9Q GAIN WILD-TYPE   23   46
        clus
vv       9Q GAIN CNV 9Q GAIN WILD-TYPE
  FEMALE           2                23
  MALE             1                46
                   vv
clus                M0 M1 MX
  9Q GAIN CNV        2  0  1
  9Q GAIN WILD-TYPE 46  1 22
D17V4, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  9Q GAIN CNV        2  0  1
  9Q GAIN WILD-TYPE 47  1 20
D17V5, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  9Q GAIN CNV        2  0  0  1
  9Q GAIN WILD-TYPE 48  8  1  7
D17V6, multiclass
    clus
vv   9Q GAIN CNV 9Q GAIN WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           1                 7
D17V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9Q GAIN CNV             2        0          1          0          0         0
  9Q GAIN WILD-TYPE      27       12         15          4          1         1
D17V8, multiclass

Clustering(18) Variable = 10p gain
D18V1, survival
                    sevent
clus2                 0  1
  10P GAIN CNV        2  3
  10P GAIN WILD-TYPE 38 23
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 5                 61 
      10P GAIN CNV 10P GAIN WILD-TYPE 
                 3                 23 
$`10P GAIN CNV`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-CC-A3MB TCGA-EP-A2KB TCGA-ES-A2HS 
       37.32        10.13         0.10         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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62         3.19         0.43        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      10P GAIN CNV 10P GAIN WILD-TYPE 
              0.10               0.07 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             37.32              90.67 
      10P GAIN CNV 10P GAIN WILD-TYPE 
             10.13              13.64 
[1] "0.1 - 37.3 (10.1)" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10P GAIN CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10P GAIN CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10P GAIN CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"       "10P GAIN CNV" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "10P GAIN CNV" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"       "10P GAIN CNV" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN CNV          3    3
  10P GAIN WILD-TYPE   22   44
        clus
vv       10P GAIN CNV 10P GAIN WILD-TYPE
  FEMALE            3                 22
  MALE              3                 44
                    vv
clus                 M0 M1 MX
  10P GAIN CNV        2  0  4
  10P GAIN WILD-TYPE 46  1 19
D18V4, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  M0            2                 46
  M1            0                  1
  MX            4                 19
                    vv
clus                 N0 N1 NX
  10P GAIN CNV        2  0  4
  10P GAIN WILD-TYPE 47  1 17
D18V5, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            4                 17
                    vv
clus                 R0 R1 R2 RX
  10P GAIN CNV        4  1  0  1
  10P GAIN WILD-TYPE 46  7  1  7
D18V6, multiclass
    clus
vv   10P GAIN CNV 10P GAIN WILD-TYPE
  R0            4                 46
  R1            1                  7
  R2            0                  1
  RX            1                  7
D18V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  10P GAIN CNV             2        0          2          0          0
  10P GAIN WILD-TYPE      27       12         14          4          1
                    vv
clus                 STAGE IVB
  10P GAIN CNV               0
  10P GAIN WILD-TYPE         1
D18V8, multiclass

Clustering(19) Variable = 12q gain
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN CNV        2  0
  12Q GAIN WILD-TYPE 38 26
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 2                 64 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 0                 26 
$`12Q GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
        6.67        34.06         6.02        29.16        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK 
        3.62         3.65         1.97         0.62         3.19         0.43 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U 
       22.85        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      12Q GAIN CNV 12Q GAIN WILD-TYPE 
              0.26               0.07 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
             38.63              90.67 
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
            19.445             13.230 
[1] "0.3 - 38.6 (19.4)" "0.1 - 90.7 (13.2)"
        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 CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"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" 
        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 CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"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" 
        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 CNV" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"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" 
[1] "Remove cluster labels:" "12Q GAIN CNV"          
clus
      12Q GAIN CNV 12Q GAIN WILD-TYPE 
                 2                 64 
        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-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"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-A1EA 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EH         TCGA-DD-A1EI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A1EJ         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-EP-A3RK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-ES-A2HS         TCGA-ES-A2HT         TCGA-FV-A2QR 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-FV-A3R3         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-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" 
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN CNV          2    1
  12Q GAIN WILD-TYPE   23   46
        clus
vv       12Q GAIN CNV 12Q GAIN WILD-TYPE
  FEMALE            2                 23
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  12Q GAIN CNV        3  0  0
  12Q GAIN WILD-TYPE 45  1 23
D19V4, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  M0            3                 45
  M1            0                  1
  MX            0                 23
                    vv
clus                 N0 N1 NX
  12Q GAIN CNV        2  0  1
  12Q GAIN WILD-TYPE 47  1 20
D19V5, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN CNV        2  0  0  1
  12Q GAIN WILD-TYPE 48  8  1  7
D19V6, multiclass
    clus
vv   12Q GAIN CNV 12Q GAIN WILD-TYPE
  R0            2                 48
  R1            0                  8
  R2            0                  1
  RX            1                  7
D19V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  12Q GAIN CNV             1        1          1          0          0
  12Q GAIN WILD-TYPE      28       11         15          4          1
                    vv
clus                 STAGE IVB
  12Q GAIN CNV               0
  12Q GAIN WILD-TYPE         1
D19V8, multiclass

Clustering(20) Variable = 15q gain
D20V1, survival
                    sevent
clus2                 0  1
  15Q GAIN CNV        2  3
  15Q GAIN WILD-TYPE 38 23
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 5                 61 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
                 3                 23 
$`15Q GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB 
       13.81         0.26         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
        1.97         0.62         3.19         0.43        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.13         1.22        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      15Q GAIN CNV 15Q GAIN WILD-TYPE 
              8.28               0.07 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             38.63              90.67 
      15Q GAIN CNV 15Q GAIN WILD-TYPE 
             23.34              11.57 
[1] "8.3 - 38.6 (23.3)" "0.1 - 90.7 (11.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"       "15Q GAIN CNV" 
        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 CNV" "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 CNV" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "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 CNV" 
        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 CNV" "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 CNV" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "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 CNV" 
        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 CNV" "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 CNV" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q GAIN WILD-TYPE"       "15Q GAIN CNV" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN CNV          3    2
  15Q GAIN WILD-TYPE   22   45
        clus
vv       15Q GAIN CNV 15Q GAIN WILD-TYPE
  FEMALE            3                 22
  MALE              2                 45
                    vv
clus                 M0 M1 MX
  15Q GAIN CNV        2  0  3
  15Q GAIN WILD-TYPE 46  1 20
D20V4, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  M0            2                 46
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  15Q GAIN CNV        2  0  3
  15Q GAIN WILD-TYPE 47  1 18
D20V5, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN CNV        4  1  0  0
  15Q GAIN WILD-TYPE 46  7  1  8
D20V6, multiclass
    clus
vv   15Q GAIN CNV 15Q GAIN WILD-TYPE
  R0            4                 46
  R1            1                  7
  R2            0                  1
  RX            0                  8
D20V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  15Q GAIN CNV             1        2          0          0          0
  15Q GAIN WILD-TYPE      28       10         16          4          1
                    vv
clus                 STAGE IVB
  15Q GAIN CNV               0
  15Q GAIN WILD-TYPE         1
D20V8, multiclass

Clustering(21) Variable = 16p gain
D21V1, survival
                    sevent
clus2                 0  1
  16P GAIN CNV        1  2
  16P GAIN WILD-TYPE 39 24
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 3                 63 
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 2                 24 
$`16P GAIN CNV`
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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       22.78         7.33         0.46        21.44        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      16P GAIN CNV 16P GAIN WILD-TYPE 
              2.60               0.07 
      16P GAIN CNV 16P GAIN WILD-TYPE 
             10.13              90.67 
      16P GAIN CNV 16P GAIN WILD-TYPE 
              5.03              13.81 
[1] "2.6 - 10.1 (5.0)"  "0.1 - 90.7 (13.8)"
        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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
[1] "hr=" "7.8"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN CNV          1    2
  16P GAIN WILD-TYPE   24   45
        clus
vv       16P GAIN CNV 16P GAIN WILD-TYPE
  FEMALE            1                 24
  MALE              2                 45
                    vv
clus                 M0 M1 MX
  16P GAIN CNV        1  0  2
  16P GAIN WILD-TYPE 47  1 21
D21V4, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  M0            1                 47
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  16P GAIN CNV        1  0  2
  16P GAIN WILD-TYPE 48  1 19
D21V5, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  N0            1                 48
  N1            0                  1
  NX            2                 19
                    vv
clus                 R0 R1 R2 RX
  16P GAIN CNV        3  0  0  0
  16P GAIN WILD-TYPE 47  8  1  8
D21V6, multiclass
    clus
vv   16P GAIN CNV 16P GAIN WILD-TYPE
  R0            3                 47
  R1            0                  8
  R2            0                  1
  RX            0                  8
D21V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  16P GAIN CNV             1        0          0          0          0
  16P GAIN WILD-TYPE      28       12         16          4          1
                    vv
clus                 STAGE IVB
  16P GAIN CNV               0
  16P GAIN WILD-TYPE         1
D21V8, multiclass
[1] "Remove cluster labels:" "16P GAIN CNV"          
clus
      16P GAIN CNV 16P GAIN WILD-TYPE 
                 1                 62 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Z         TCGA-BC-A216         TCGA-BC-A217 
"16P GAIN WILD-TYPE" "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-5260         TCGA-CC-5261         TCGA-CC-5262 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-5264         TCGA-CC-A1HT 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11B         TCGA-DD-A11C         TCGA-DD-A11D 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1E9         TCGA-DD-A1EA         TCGA-DD-A1EB 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EC         TCGA-DD-A1ED         TCGA-DD-A1EE 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EH         TCGA-DD-A1EI         TCGA-DD-A1EJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A1EL         TCGA-EP-A12J         TCGA-EP-A26S 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A2KA         TCGA-EP-A2KB         TCGA-EP-A2KC 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HS 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-ES-A2HT         TCGA-FV-A2QR         TCGA-FV-A3I1 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-FV-A3R3         TCGA-G3-A25S         TCGA-G3-A25T 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         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" 

Clustering(22) Variable = 17p gain
D22V1, survival
                    sevent
clus2                 0  1
  17P GAIN CNV        1  2
  17P GAIN WILD-TYPE 39 24
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 3                 63 
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 24 
$`17P GAIN CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
        6.67        34.06         6.02        29.16        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.62         3.65         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      17P GAIN CNV 17P GAIN WILD-TYPE 
              1.97               0.07 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             37.32              90.67 
      17P GAIN CNV 17P GAIN WILD-TYPE 
             22.85              12.82 
[1] "2.0 - 37.3 (22.9)" "0.1 - 90.7 (12.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"       "17P GAIN CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17P GAIN CNV" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"       "17P GAIN CNV" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN CNV          2    1
  17P GAIN WILD-TYPE   23   46
        clus
vv       17P GAIN CNV 17P GAIN WILD-TYPE
  FEMALE            2                 23
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  17P GAIN CNV        0  0  3
  17P GAIN WILD-TYPE 48  1 20
D22V4, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  M0            0                 48
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  17P GAIN CNV        0  0  3
  17P GAIN WILD-TYPE 49  1 18
D22V5, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  N0            0                 49
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  17P GAIN CNV        2  1  0  0
  17P GAIN WILD-TYPE 48  7  1  8
D22V6, multiclass
    clus
vv   17P GAIN CNV 17P GAIN WILD-TYPE
  R0            2                 48
  R1            1                  7
  R2            0                  1
  RX            0                  8
D22V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17P GAIN CNV             2        0          0          0          0
  17P GAIN WILD-TYPE      27       12         16          4          1
                    vv
clus                 STAGE IVB
  17P GAIN CNV               0
  17P GAIN WILD-TYPE         1
D22V8, multiclass
[1] "Remove cluster labels:" "17P GAIN CNV"          
clus
      17P GAIN CNV 17P GAIN WILD-TYPE 
                 2                 61 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Z         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-5260         TCGA-CC-5261         TCGA-CC-5262 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-5264         TCGA-CC-A1HT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-A1EA 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EB         TCGA-DD-A1EC         TCGA-DD-A1ED 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EE         TCGA-DD-A1EH         TCGA-DD-A1EI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A1EJ         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-A2KC 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3JL         TCGA-EP-A3RK         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I1         TCGA-FV-A3R3 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" 

Clustering(23) Variable = 17q gain
D23V1, survival
                    sevent
clus2                 0  1
  17Q GAIN CNV        7  9
  17Q GAIN WILD-TYPE 33 17
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                16                 50 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
                 9                 17 
$`17Q GAIN CNV`
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-DD-A1EA TCGA-EP-A2KB TCGA-ES-A2HS 
       13.81         4.24        37.74        79.36         1.97        22.85 
TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CK 
       40.47        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-CC-A3MA 
       69.57        37.61         0.26         8.28         0.07         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10         0.13        55.17        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-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       29.16        13.64         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        3.19         0.43        14.40        19.07         0.13         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       38.63        14.27        44.68        14.86         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ 
        5.88         4.47 

      17Q GAIN CNV 17Q GAIN WILD-TYPE 
              0.89               0.07 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
             79.36              90.67 
      17Q GAIN CNV 17Q GAIN WILD-TYPE 
            13.315             12.605 
[1] "0.9 - 79.4 (13.3)" "0.1 - 90.7 (12.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
      "17Q GAIN CNV"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"       "17Q GAIN CNV" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17Q GAIN CNV" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"       "17Q GAIN CNV" 
[1] "hr=" "1.9"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN CNV          7   10
  17Q GAIN WILD-TYPE   18   37
        clus
vv       17Q GAIN CNV 17Q GAIN WILD-TYPE
  FEMALE            7                 18
  MALE             10                 37
                    vv
clus                 M0 M1 MX
  17Q GAIN CNV       10  0  7
  17Q GAIN WILD-TYPE 38  1 16
D23V4, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  M0           10                 38
  M1            0                  1
  MX            7                 16
                    vv
clus                 N0 N1 NX
  17Q GAIN CNV        9  0  7
  17Q GAIN WILD-TYPE 40  1 14
D23V5, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  N0            9                 40
  N1            0                  1
  NX            7                 14
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN CNV       12  3  0  2
  17Q GAIN WILD-TYPE 38  5  1  6
D23V6, multiclass
    clus
vv   17Q GAIN CNV 17Q GAIN WILD-TYPE
  R0           12                 38
  R1            3                  5
  R2            0                  1
  RX            2                  6
D23V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17Q GAIN CNV             6        4          2          1          0
  17Q GAIN WILD-TYPE      23        8         14          3          1
                    vv
clus                 STAGE IVB
  17Q GAIN CNV               0
  17Q GAIN WILD-TYPE         1
D23V8, multiclass

Clustering(24) Variable = 18p gain
D24V1, survival
                    sevent
clus2                 0  1
  18P GAIN CNV        2  1
  18P GAIN WILD-TYPE 38 25
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 3                 63 
      18P GAIN CNV 18P GAIN WILD-TYPE 
                 1                 25 
$`18P GAIN CNV`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 
        4.24         0.13        55.17 

$`18P 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-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      18P GAIN CNV 18P GAIN WILD-TYPE 
              0.13               0.07 
      18P GAIN CNV 18P GAIN WILD-TYPE 
             55.17              90.67 
      18P GAIN CNV 18P GAIN WILD-TYPE 
              4.24              13.64 
[1] "0.1 - 55.2 (4.2)"  "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "18P GAIN CNV" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18P GAIN CNV"       "18P GAIN CNV" "18P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" "18P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN CNV          1    2
  18P GAIN WILD-TYPE   24   45
        clus
vv       18P GAIN CNV 18P GAIN WILD-TYPE
  FEMALE            1                 24
  MALE              2                 45
                    vv
clus                 M0 M1 MX
  18P GAIN CNV        3  0  0
  18P GAIN WILD-TYPE 45  1 23
D24V4, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  M0            3                 45
  M1            0                  1
  MX            0                 23
                    vv
clus                 N0 N1 NX
  18P GAIN CNV        3  0  0
  18P GAIN WILD-TYPE 46  1 21
D24V5, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  N0            3                 46
  N1            0                  1
  NX            0                 21
                    vv
clus                 R0 R1 R2 RX
  18P GAIN CNV        2  0  0  1
  18P GAIN WILD-TYPE 48  8  1  7
D24V6, multiclass
    clus
vv   18P GAIN CNV 18P GAIN WILD-TYPE
  R0            2                 48
  R1            0                  8
  R2            0                  1
  RX            1                  7
D24V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18P GAIN CNV             0        1          2          0          0
  18P GAIN WILD-TYPE      29       11         14          4          1
                    vv
clus                 STAGE IVB
  18P GAIN CNV               0
  18P GAIN WILD-TYPE         1
D24V8, multiclass

Clustering(25) Variable = 18q gain
D25V1, survival
                    sevent
clus2                 0  1
  18Q GAIN CNV        3  1
  18Q GAIN WILD-TYPE 37 25
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 4                 62 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
                 1                 25 
$`18Q GAIN CNV`
TCGA-CC-5263 TCGA-CC-A3MC TCGA-DD-A113 TCGA-G3-A25X 
        4.24         0.13        55.17        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-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.10        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       12.82        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      18Q GAIN CNV 18Q GAIN WILD-TYPE 
              0.13               0.07 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             55.17              90.67 
      18Q GAIN CNV 18Q GAIN WILD-TYPE 
             24.46              13.23 
[1] "0.1 - 55.2 (24.5)" "0.1 - 90.7 (13.2)"
        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-CC-A3MA         TCGA-CC-A3MB 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18Q GAIN CNV"       "18Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18Q GAIN CNV"       "18Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
      "18Q GAIN CNV" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "18Q GAIN CNV"       "18Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN CNV          1    3
  18Q GAIN WILD-TYPE   24   44
        clus
vv       18Q GAIN CNV 18Q GAIN WILD-TYPE
  FEMALE            1                 24
  MALE              3                 44
                    vv
clus                 M0 M1 MX
  18Q GAIN CNV        4  0  0
  18Q GAIN WILD-TYPE 44  1 23
D25V4, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  M0            4                 44
  M1            0                  1
  MX            0                 23
                    vv
clus                 N0 N1 NX
  18Q GAIN CNV        4  0  0
  18Q GAIN WILD-TYPE 45  1 21
D25V5, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  N0            4                 45
  N1            0                  1
  NX            0                 21
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN CNV        3  0  0  1
  18Q GAIN WILD-TYPE 47  8  1  7
D25V6, multiclass
    clus
vv   18Q GAIN CNV 18Q GAIN WILD-TYPE
  R0            3                 47
  R1            0                  8
  R2            0                  1
  RX            1                  7
D25V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18Q GAIN CNV             0        2          2          0          0
  18Q GAIN WILD-TYPE      29       10         14          4          1
                    vv
clus                 STAGE IVB
  18Q GAIN CNV               0
  18Q GAIN WILD-TYPE         1
D25V8, multiclass

Clustering(26) Variable = 19p gain
D26V1, survival
                    sevent
clus2                 0  1
  19P GAIN CNV        4  1
  19P GAIN WILD-TYPE 36 25
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 5                 61 
      19P GAIN CNV 19P GAIN WILD-TYPE 
                 1                 25 
$`19P GAIN CNV`
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       55.17        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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        4.24         0.07         0.10         0.13        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29         7.33         2.60         0.46        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       90.67        79.36        66.31        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62         3.19         0.43        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      19P GAIN CNV 19P GAIN WILD-TYPE 
              1.97               0.07 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             55.17              90.67 
      19P GAIN CNV 19P GAIN WILD-TYPE 
             22.78              11.57 
[1] "2.0 - 55.2 (22.8)" "0.1 - 90.7 (11.6)"
        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-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"       "19P GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19P GAIN CNV" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"       "19P GAIN CNV" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN CNV          4    1
  19P GAIN WILD-TYPE   21   46
        clus
vv       19P GAIN CNV 19P GAIN WILD-TYPE
  FEMALE            4                 21
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  19P GAIN CNV        3  0  2
  19P GAIN WILD-TYPE 45  1 21
D26V4, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  M0            3                 45
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  19P GAIN CNV        3  0  2
  19P GAIN WILD-TYPE 46  1 19
D26V5, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  N0            3                 46
  N1            0                  1
  NX            2                 19
                    vv
clus                 R0 R1 R2 RX
  19P GAIN CNV        5  0  0  0
  19P GAIN WILD-TYPE 45  8  1  8
D26V6, multiclass
    clus
vv   19P GAIN CNV 19P GAIN WILD-TYPE
  R0            5                 45
  R1            0                  8
  R2            0                  1
  RX            0                  8
D26V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19P GAIN CNV             4        1          0          0          0
  19P GAIN WILD-TYPE      25       11         16          4          1
                    vv
clus                 STAGE IVB
  19P GAIN CNV               0
  19P GAIN WILD-TYPE         1
D26V8, multiclass

Clustering(27) Variable = 19q gain
D27V1, survival
                    sevent
clus2                 0  1
  19Q GAIN CNV        5  2
  19Q GAIN WILD-TYPE 35 24
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 7                 59 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
                 2                 24 
$`19Q GAIN CNV`
TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       10.13        55.17        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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        37.74        83.57        53.29 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       79.36        66.31        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       29.16        13.64         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        3.19         0.43        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      19Q GAIN CNV 19Q GAIN WILD-TYPE 
              1.97               0.07 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             55.17              90.67 
      19Q GAIN CNV 19Q GAIN WILD-TYPE 
             22.78              11.57 
[1] "2.0 - 55.2 (22.8)" "0.1 - 90.7 (11.6)"
        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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"       "19Q GAIN CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "19Q GAIN CNV" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"       "19Q GAIN CNV" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN CNV          5    2
  19Q GAIN WILD-TYPE   20   45
        clus
vv       19Q GAIN CNV 19Q GAIN WILD-TYPE
  FEMALE            5                 20
  MALE              2                 45
                    vv
clus                 M0 M1 MX
  19Q GAIN CNV        4  0  3
  19Q GAIN WILD-TYPE 44  1 20
D27V4, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  M0            4                 44
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  19Q GAIN CNV        4  0  3
  19Q GAIN WILD-TYPE 45  1 18
D27V5, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  N0            4                 45
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN CNV        7  0  0  0
  19Q GAIN WILD-TYPE 43  8  1  8
D27V6, multiclass
    clus
vv   19Q GAIN CNV 19Q GAIN WILD-TYPE
  R0            7                 43
  R1            0                  8
  R2            0                  1
  RX            0                  8
D27V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19Q GAIN CNV             4        2          0          0          0
  19Q GAIN WILD-TYPE      25       10         16          4          1
                    vv
clus                 STAGE IVB
  19Q GAIN CNV               0
  19Q GAIN WILD-TYPE         1
D27V8, multiclass

Clustering(28) Variable = 20p gain
D28V1, survival
                    sevent
clus2                 0  1
  20P GAIN CNV        6  5
  20P GAIN WILD-TYPE 34 21
      20P GAIN CNV 20P GAIN WILD-TYPE 
                11                 55 
      20P GAIN CNV 20P GAIN WILD-TYPE 
                 5                 21 
$`20P GAIN CNV`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-CC-A3MB TCGA-DD-A118 
       48.99        37.32        10.13         0.26         0.10        22.78 
TCGA-DD-A11B TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
        0.46         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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        8.28         0.07         4.24         0.07         0.13        55.17 
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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
        6.67        34.06         6.02        29.16        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
        3.62         3.65         0.62         0.43        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.13        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      20P GAIN CNV 20P GAIN WILD-TYPE 
              0.10               0.07 
      20P GAIN CNV 20P GAIN WILD-TYPE 
             48.99              90.67 
      20P GAIN CNV 20P GAIN WILD-TYPE 
              3.19              13.81 
[1] "0.1 - 49.0 (3.2)"  "0.1 - 90.7 (13.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20P GAIN CNV" "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 CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        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-A3CH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20P GAIN CNV" "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 CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        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-A3CH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20P GAIN CNV" "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 CNV" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20P GAIN CNV" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"       "20P GAIN CNV" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"       "20P GAIN CNV" 
        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-A3CH 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN CNV          6    7
  20P GAIN WILD-TYPE   19   40
        clus
vv       20P GAIN CNV 20P GAIN WILD-TYPE
  FEMALE            6                 19
  MALE              7                 40
                    vv
clus                 M0 M1 MX
  20P GAIN CNV        8  0  5
  20P GAIN WILD-TYPE 40  1 18
D28V4, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  M0            8                 40
  M1            0                  1
  MX            5                 18
                    vv
clus                 N0 N1 NX
  20P GAIN CNV        7  0  6
  20P GAIN WILD-TYPE 42  1 15
D28V5, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  N0            7                 42
  N1            0                  1
  NX            6                 15
                    vv
clus                 R0 R1 R2 RX
  20P GAIN CNV        6  3  0  3
  20P GAIN WILD-TYPE 44  5  1  5
D28V6, multiclass
    clus
vv   20P GAIN CNV 20P GAIN WILD-TYPE
  R0            6                 44
  R1            3                  5
  R2            0                  1
  RX            3                  5
D28V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN CNV             7        1          3          0          0
  20P GAIN WILD-TYPE      22       11         13          4          1
                    vv
clus                 STAGE IVB
  20P GAIN CNV               0
  20P GAIN WILD-TYPE         1
D28V8, multiclass

Clustering(29) Variable = 20q gain
D29V1, survival
                    sevent
clus2                 0  1
  20Q GAIN CNV        7  5
  20Q GAIN WILD-TYPE 33 21
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                12                 54 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
                 5                 21 
$`20Q GAIN CNV`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-CC-A3MB TCGA-DD-A118 
       48.99        37.32        10.13         0.26         0.10        22.78 
TCGA-DD-A11B TCGA-DD-A11C TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
        0.46        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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        8.28         0.07         4.24         0.07         0.13        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D 
       37.74        83.57        53.29         7.33         2.60        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        3.65         0.62         0.43        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         6.31         5.88         4.47         0.89 

      20Q GAIN CNV 20Q GAIN WILD-TYPE 
              0.10               0.07 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             48.99              90.67 
      20Q GAIN CNV 20Q GAIN WILD-TYPE 
             6.660             13.725 
[1] "0.1 - 49.0 (6.7)"  "0.1 - 90.7 (13.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20Q GAIN CNV" "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 CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        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-A3CH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20Q GAIN CNV" "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 CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        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-A3CH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "20Q GAIN CNV" "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 CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "20Q GAIN CNV" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"       "20Q GAIN CNV" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"       "20Q GAIN CNV" 
        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-A3CH 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN CNV          6    8
  20Q GAIN WILD-TYPE   19   39
        clus
vv       20Q GAIN CNV 20Q GAIN WILD-TYPE
  FEMALE            6                 19
  MALE              8                 39
                    vv
clus                 M0 M1 MX
  20Q GAIN CNV        9  0  5
  20Q GAIN WILD-TYPE 39  1 18
D29V4, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  M0            9                 39
  M1            0                  1
  MX            5                 18
                    vv
clus                 N0 N1 NX
  20Q GAIN CNV        8  0  6
  20Q GAIN WILD-TYPE 41  1 15
D29V5, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  N0            8                 41
  N1            0                  1
  NX            6                 15
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN CNV        6  3  0  4
  20Q GAIN WILD-TYPE 44  5  1  4
D29V6, multiclass
    clus
vv   20Q GAIN CNV 20Q GAIN WILD-TYPE
  R0            6                 44
  R1            3                  5
  R2            0                  1
  RX            4                  4
D29V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN CNV             8        1          3          0          0
  20Q GAIN WILD-TYPE      21       11         13          4          1
                    vv
clus                 STAGE IVB
  20Q GAIN CNV               0
  20Q GAIN WILD-TYPE         1
D29V8, multiclass

Clustering(30) Variable = 21q gain
D30V1, survival
                    sevent
clus2                 0  1
  21Q GAIN CNV        3  1
  21Q GAIN WILD-TYPE 37 25
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 4                 62 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
                 1                 25 
$`21Q GAIN CNV`
TCGA-DD-A113 TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25T 
       55.17         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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 
        4.24         0.07         0.10         0.13        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
        6.67        34.06         6.02        29.16        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.62         3.65         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13         1.22        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       44.68        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      21Q GAIN CNV 21Q GAIN WILD-TYPE 
              1.97               0.07 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
             55.17              90.67 
      21Q GAIN CNV 21Q GAIN WILD-TYPE 
            30.740             12.195 
[1] "2.0 - 55.2 (30.7)" "0.1 - 90.7 (12.2)"
        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-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "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-CC-A3MA         TCGA-CC-A3MB 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "21Q GAIN CNV" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"       "21Q GAIN CNV" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "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-A3CH 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN CNV          3    1
  21Q GAIN WILD-TYPE   22   46
        clus
vv       21Q GAIN CNV 21Q GAIN WILD-TYPE
  FEMALE            3                 22
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  21Q GAIN CNV        2  0  2
  21Q GAIN WILD-TYPE 46  1 21
D30V4, multiclass
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  M0            2                 46
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  21Q GAIN CNV        2  0  2
  21Q GAIN WILD-TYPE 47  1 19
D30V5, multiclass
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            2                 19
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN CNV        4  0  0  0
  21Q GAIN WILD-TYPE 46  8  1  8
D30V6, multiclass
    clus
vv   21Q GAIN CNV 21Q GAIN WILD-TYPE
  R0            4                 46
  R1            0                  8
  R2            0                  1
  RX            0                  8
D30V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN CNV             2        2          0          0          0
  21Q GAIN WILD-TYPE      27       10         16          4          1
                    vv
clus                 STAGE IVB
  21Q GAIN CNV               0
  21Q GAIN WILD-TYPE         1
D30V8, multiclass

Clustering(31) Variable = 22q gain
D31V1, survival
                    sevent
clus2                 0  1
  22Q GAIN CNV        3  5
  22Q GAIN WILD-TYPE 37 21
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 8                 58 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
                 5                 21 
$`22Q GAIN CNV`
TCGA-BC-A10R TCGA-BC-A112 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ 
       10.13         5.03         0.10        22.78        51.25        29.16 
TCGA-ES-A2HS TCGA-FV-A2QR 
       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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.13        55.17        37.74        83.57        53.29         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        21.44        90.67        79.36        66.31 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL 
       19.76        53.52         6.67        34.06         6.02        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-EP-A3RK TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.43        14.40         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      22Q GAIN CNV 22Q GAIN WILD-TYPE 
              0.10               0.07 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
             51.25              90.67 
      22Q GAIN CNV 22Q GAIN WILD-TYPE 
            20.925             12.195 
[1] "0.1 - 51.2 (20.9)" "0.1 - 90.7 (12.2)"
        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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        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 CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "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-A3CH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        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 CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "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-A3CH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"       "22Q GAIN CNV" 
        TCGA-CC-A3MC         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 CNV" 
        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 CNV" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q GAIN WILD-TYPE"       "22Q GAIN CNV" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "22Q GAIN CNV" "22Q GAIN WILD-TYPE" "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-A3CH 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN CNV          4    4
  22Q GAIN WILD-TYPE   21   43
        clus
vv       22Q GAIN CNV 22Q GAIN WILD-TYPE
  FEMALE            4                 21
  MALE              4                 43
                    vv
clus                 M0 M1 MX
  22Q GAIN CNV        5  0  3
  22Q GAIN WILD-TYPE 43  1 20
D31V4, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  M0            5                 43
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  22Q GAIN CNV        4  1  3
  22Q GAIN WILD-TYPE 45  0 18
D31V5, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  N0            4                 45
  N1            1                  0
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN CNV        7  0  0  1
  22Q GAIN WILD-TYPE 43  8  1  7
D31V6, multiclass
    clus
vv   22Q GAIN CNV 22Q GAIN WILD-TYPE
  R0            7                 43
  R1            0                  8
  R2            0                  1
  RX            1                  7
D31V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN CNV             4        0          1          0          1
  22Q GAIN WILD-TYPE      25       12         15          4          0
                    vv
clus                 STAGE IVB
  22Q GAIN CNV               0
  22Q GAIN WILD-TYPE         1
D31V8, multiclass

Clustering(32) Variable = Xq gain
D32V1, survival
                   sevent
clus2                0  1
  XQ GAIN CNV        2  2
  XQ GAIN WILD-TYPE 38 24
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                4                62 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
                2                24 
$`XQ GAIN CNV`
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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       22.78         7.33         0.46        21.44        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        6.02        29.16        13.64         3.62         3.65         1.97 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         3.19         0.43        22.85        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
        0.13         1.22        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       44.68        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      XQ GAIN CNV XQ GAIN WILD-TYPE 
             1.12              0.07 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            27.52             90.67 
      XQ GAIN CNV XQ GAIN WILD-TYPE 
            3.420            13.725 
[1] "1.1 - 27.5 (3.4)"  "0.1 - 90.7 (13.7)"
       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 CNV" "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 CNV" "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-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "XQ GAIN CNV" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"       "XQ GAIN CNV" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
[1] "hr=" "3.1"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN CNV          1    3
  XQ GAIN WILD-TYPE   24   44
        clus
vv       XQ GAIN CNV XQ GAIN WILD-TYPE
  FEMALE           1                24
  MALE             3                44
                   vv
clus                M0 M1 MX
  XQ GAIN CNV        1  0  3
  XQ GAIN WILD-TYPE 47  1 20
D32V4, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  M0           1                47
  M1           0                 1
  MX           3                20
                   vv
clus                N0 N1 NX
  XQ GAIN CNV        2  0  2
  XQ GAIN WILD-TYPE 47  1 19
D32V5, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  XQ GAIN CNV        3  1  0  0
  XQ GAIN WILD-TYPE 47  7  1  8
D32V6, multiclass
    clus
vv   XQ GAIN CNV XQ GAIN WILD-TYPE
  R0           3                47
  R1           1                 7
  R2           0                 1
  RX           0                 8
D32V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  XQ GAIN CNV             3        0          0          0          0         0
  XQ GAIN WILD-TYPE      26       12         16          4          1         1
D32V8, multiclass

Clustering(33) Variable = 1p loss
D33V1, survival
                   sevent
clus2                0  1
  1P LOSS CNV        7  5
  1P LOSS WILD-TYPE 33 21
      1P LOSS CNV 1P LOSS WILD-TYPE 
               12                54 
      1P LOSS CNV 1P LOSS WILD-TYPE 
                5                21 
$`1P LOSS CNV`
TCGA-BC-A10S TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D 
       46.78         0.10        55.17        22.78         0.46        51.25 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-G3-A25U 
       34.06        29.16         1.97         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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 
        0.07         0.13        37.74        83.57        53.29         7.33 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60        21.44        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       53.52         6.67         6.02        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        3.65         3.19         0.43        14.40        19.07         0.13 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        38.63        14.27        12.82        44.68        14.86 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         6.31         5.88         4.47         0.89 

      1P LOSS CNV 1P LOSS WILD-TYPE 
             0.10              0.07 
      1P LOSS CNV 1P LOSS WILD-TYPE 
            55.17             90.67 
      1P LOSS CNV 1P LOSS WILD-TYPE 
           26.005            10.850 
[1] "0.1 - 55.2 (26.0)" "0.1 - 90.7 (10.9)"
       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 CNV" "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-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1P LOSS WILD-TYPE"       "1P LOSS CNV"       "1P LOSS CNV" "1P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1P LOSS WILD-TYPE"       "1P LOSS CNV" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"       "1P LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS CNV          6    7
  1P LOSS WILD-TYPE   19   40
        clus
vv       1P LOSS CNV 1P LOSS WILD-TYPE
  FEMALE           6                19
  MALE             7                40
                   vv
clus                M0 M1 MX
  1P LOSS CNV        9  0  4
  1P LOSS WILD-TYPE 39  1 19
D33V4, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  M0           9                39
  M1           0                 1
  MX           4                19
                   vv
clus                N0 N1 NX
  1P LOSS CNV        8  1  4
  1P LOSS WILD-TYPE 41  0 17
D33V5, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  N0           8                41
  N1           1                 0
  NX           4                17
                   vv
clus                R0 R1 R2 RX
  1P LOSS CNV       11  0  0  2
  1P LOSS WILD-TYPE 39  8  1  6
D33V6, multiclass
    clus
vv   1P LOSS CNV 1P LOSS WILD-TYPE
  R0          11                39
  R1           0                 8
  R2           0                 1
  RX           2                 6
D33V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1P LOSS CNV             7        2          1          1          1         0
  1P LOSS WILD-TYPE      22       10         15          3          0         1
D33V8, multiclass

Clustering(34) Variable = 1q loss
D34V1, survival
                   sevent
clus2                0  1
  1Q LOSS CNV        3  2
  1Q LOSS WILD-TYPE 37 24
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                5                61 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
                2                24 
$`1Q LOSS CNV`
TCGA-BC-A10S TCGA-CC-A3MB TCGA-DD-A1EJ TCGA-ES-A2HS TCGA-G3-A25U 
       46.78         0.10        29.16        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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.13        55.17        37.74        83.57        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06         6.02        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
        1.97         0.62         3.19         0.43        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
        0.13         1.22        38.63        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      1Q LOSS CNV 1Q LOSS WILD-TYPE 
             0.10              0.07 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
            46.78             90.67 
      1Q LOSS CNV 1Q LOSS WILD-TYPE 
            29.16             11.57 
[1] "0.1 - 46.8 (29.2)" "0.1 - 90.7 (11.6)"
       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 CNV" "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-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"1Q LOSS WILD-TYPE"       "1Q LOSS CNV" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"       "1Q LOSS CNV" 
       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-A3CH        TCGA-G3-A3CI 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS CNV          2    3
  1Q LOSS WILD-TYPE   23   44
        clus
vv       1Q LOSS CNV 1Q LOSS WILD-TYPE
  FEMALE           2                23
  MALE             3                44
                   vv
clus                M0 M1 MX
  1Q LOSS CNV        3  0  2
  1Q LOSS WILD-TYPE 45  1 21
D34V4, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  M0           3                45
  M1           0                 1
  MX           2                21
                   vv
clus                N0 N1 NX
  1Q LOSS CNV        2  1  2
  1Q LOSS WILD-TYPE 47  0 19
D34V5, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  N0           2                47
  N1           1                 0
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  1Q LOSS CNV        5  0  0  0
  1Q LOSS WILD-TYPE 45  8  1  8
D34V6, multiclass
    clus
vv   1Q LOSS CNV 1Q LOSS WILD-TYPE
  R0           5                45
  R1           0                 8
  R2           0                 1
  RX           0                 8
D34V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1Q LOSS CNV             2        0          1          0          1         0
  1Q LOSS WILD-TYPE      27       12         15          4          0         1
D34V8, multiclass

Clustering(35) Variable = 2p loss
D35V1, survival
                   sevent
clus2                0  1
  2P LOSS CNV        2  0
  2P LOSS WILD-TYPE 38 26
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                64 
      2P LOSS CNV 2P LOSS WILD-TYPE 
                0                26 
$`2P LOSS CNV`
TCGA-BC-A3KF TCGA-DD-A11C 
        0.26        21.44 

$`2P 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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.29        22.78         7.33         2.60         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.65         1.97         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      2P LOSS CNV 2P LOSS WILD-TYPE 
             0.26              0.07 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            21.44             90.67 
      2P LOSS CNV 2P LOSS WILD-TYPE 
            10.85             13.23 
[1] "0.3 - 21.4 (10.9)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"       "2P LOSS CNV" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                64 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA        TCGA-CC-A3MB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11B        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3R3        TCGA-G3-A25S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V        TCGA-G3-A25W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D35V2, continuous
[1] "Remove cluster labels:" "2P LOSS CNV"           
clus
      2P LOSS CNV 2P LOSS WILD-TYPE 
                2                68 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-5264        TCGA-CC-A1HT        TCGA-CC-A3MA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11D        TCGA-DD-A1E9 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A3R3        TCGA-G3-A25S 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V        TCGA-G3-A25W 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-G3-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS CNV          2    1
  2P LOSS WILD-TYPE   23   46
        clus
vv       2P LOSS CNV 2P LOSS WILD-TYPE
  FEMALE           2                23
  MALE             1                46
                   vv
clus                M0 M1 MX
  2P LOSS CNV        2  0  1
  2P LOSS WILD-TYPE 46  1 22
D35V4, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  2P LOSS CNV        2  0  1
  2P LOSS WILD-TYPE 47  1 20
D35V5, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  2P LOSS CNV        2  0  0  1
  2P LOSS WILD-TYPE 48  8  1  7
D35V6, multiclass
    clus
vv   2P LOSS CNV 2P LOSS WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           1                 7
D35V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2P LOSS CNV             2        1          0          0          0         0
  2P LOSS WILD-TYPE      27       11         16          4          1         1
D35V8, multiclass

Clustering(36) Variable = 2q loss
D36V1, survival
                   sevent
clus2                0  1
  2Q LOSS CNV        2  0
  2Q LOSS WILD-TYPE 38 26
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2                64 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                0                26 
$`2Q LOSS CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.29        22.78         7.33         2.60         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.65         1.97         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      2Q LOSS CNV 2Q LOSS WILD-TYPE 
             0.26              0.07 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            21.44             90.67 
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
            10.85             13.23 
[1] "0.3 - 21.4 (10.9)" "0.1 - 90.7 (13.2)"
       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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        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-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        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-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" "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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        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-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        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-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" "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 CNV" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        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-A11C        TCGA-DD-A11D 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"       "2Q LOSS CNV" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        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-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
[1] "Remove cluster labels:" "2Q LOSS CNV"           
clus
      2Q LOSS CNV 2Q LOSS WILD-TYPE 
                2                64 
       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-CC-A3MA        TCGA-CC-A3MB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114        TCGA-DD-A115 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119        TCGA-DD-A11A 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11B        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        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-EP-A3RK        TCGA-ES-A2HS 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI        TCGA-G3-A3CJ        TCGA-G3-A3CK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS CNV          2    2
  2Q LOSS WILD-TYPE   23   45
        clus
vv       2Q LOSS CNV 2Q LOSS WILD-TYPE
  FEMALE           2                23
  MALE             2                45
                   vv
clus                M0 M1 MX
  2Q LOSS CNV        3  0  1
  2Q LOSS WILD-TYPE 45  1 22
D36V4, multiclass
    clus
vv   2Q LOSS CNV 2Q LOSS WILD-TYPE
  M0           3                45
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  2Q LOSS CNV        3  0  1
  2Q LOSS WILD-TYPE 46  1 20
D36V5, multiclass
    clus
vv   2Q LOSS CNV 2Q LOSS WILD-TYPE
  N0           3                46
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  2Q LOSS CNV        2  0  0  2
  2Q LOSS WILD-TYPE 48  8  1  6
D36V6, multiclass
    clus
vv   2Q LOSS CNV 2Q LOSS WILD-TYPE
  R0           2                48
  R1           0                 8
  R2           0                 1
  RX           2                 6
D36V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2Q LOSS CNV             2        1          1          0          0         0
  2Q LOSS WILD-TYPE      27       11         15          4          1         1
D36V8, multiclass

Clustering(37) Variable = 3p loss
D37V1, survival
                   sevent
clus2                0  1
  3P LOSS CNV        5  2
  3P LOSS WILD-TYPE 35 24
      3P LOSS CNV 3P LOSS WILD-TYPE 
                7                59 
      3P LOSS CNV 3P LOSS WILD-TYPE 
                2                24 
$`3P LOSS CNV`
TCGA-BC-A112 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 
        5.03         4.24         0.07         0.10        55.17        22.78 
TCGA-G3-A25T 
       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-CC-A3MC 
       37.61        13.81         0.26         8.28         0.07         0.13 
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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        0.43        22.85        14.40        19.07         0.13         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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      3P LOSS CNV 3P LOSS WILD-TYPE 
             0.07              0.07 
      3P LOSS CNV 3P LOSS WILD-TYPE 
            55.17             90.67 
      3P LOSS CNV 3P LOSS WILD-TYPE 
             5.03             13.64 
[1] "0.1 - 55.2 (5.0)"  "0.1 - 90.7 (13.6)"
       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 CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" "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 CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" "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 CNV" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV"       "3P LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "3P LOSS CNV" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"       "3P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS CNV          3    4
  3P LOSS WILD-TYPE   22   43
        clus
vv       3P LOSS CNV 3P LOSS WILD-TYPE
  FEMALE           3                22
  MALE             4                43
                   vv
clus                M0 M1 MX
  3P LOSS CNV        6  0  1
  3P LOSS WILD-TYPE 42  1 22
D37V4, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  M0           6                42
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  3P LOSS CNV        6  0  1
  3P LOSS WILD-TYPE 43  1 20
D37V5, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  N0           6                43
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  3P LOSS CNV        6  0  0  1
  3P LOSS WILD-TYPE 44  8  1  7
D37V6, multiclass
    clus
vv   3P LOSS CNV 3P LOSS WILD-TYPE
  R0           6                44
  R1           0                 8
  R2           0                 1
  RX           1                 7
D37V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3P LOSS CNV             1        2          3          0          0         0
  3P LOSS WILD-TYPE      28       10         13          4          1         1
D37V8, multiclass

Clustering(38) Variable = 3q loss
D38V1, survival
                   sevent
clus2                0  1
  3Q LOSS CNV        2  1
  3Q LOSS WILD-TYPE 38 25
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                3                63 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                1                25 
$`3Q LOSS CNV`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A118 
        5.03        55.17        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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.07         0.10         0.13        37.74        83.57        53.29 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      3Q LOSS CNV 3Q LOSS WILD-TYPE 
             5.03              0.07 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            55.17             90.67 
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
            22.78             12.82 
[1] "5.0 - 55.2 (22.8)" "0.1 - 90.7 (12.8)"
       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 CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" "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 CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" "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 CNV" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"       "3Q LOSS CNV" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS CNV          2    1
  3Q LOSS WILD-TYPE   23   46
        clus
vv       3Q LOSS CNV 3Q LOSS WILD-TYPE
  FEMALE           2                23
  MALE             1                46
                   vv
clus                M0 M1 MX
  3Q LOSS CNV        2  0  1
  3Q LOSS WILD-TYPE 46  1 22
D38V4, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  3Q LOSS CNV        2  0  1
  3Q LOSS WILD-TYPE 47  1 20
D38V5, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           1                20
                   vv
clus                R0 R1 R2 RX
  3Q LOSS CNV        3  0  0  0
  3Q LOSS WILD-TYPE 47  8  1  8
D38V6, multiclass
    clus
vv   3Q LOSS CNV 3Q LOSS WILD-TYPE
  R0           3                47
  R1           0                 8
  R2           0                 1
  RX           0                 8
D38V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3Q LOSS CNV             1        1          0          0          0         0
  3Q LOSS WILD-TYPE      28       11         16          4          1         1
D38V8, multiclass
[1] "Remove cluster labels:" "3Q LOSS CNV"           
clus
      3Q LOSS CNV 3Q LOSS WILD-TYPE 
                2                61 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10X        TCGA-BC-A10Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF        TCGA-BC-A3KG 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5260        TCGA-CC-5261        TCGA-CC-5262 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-5263        TCGA-CC-5264        TCGA-CC-A1HT        TCGA-CC-A3MA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A114        TCGA-DD-A115 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A116        TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ        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-EP-A3RK        TCGA-ES-A2HS 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3I1        TCGA-FV-A3R3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A3CG        TCGA-G3-A3CH        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" 

Clustering(39) Variable = 4p loss
D39V1, survival
                   sevent
clus2                0  1
  4P LOSS CNV        4  4
  4P LOSS WILD-TYPE 36 22
      4P LOSS CNV 4P LOSS WILD-TYPE 
                8                58 
      4P LOSS CNV 4P LOSS WILD-TYPE 
                4                22 
$`4P LOSS CNV`
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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06         6.02        29.16         4.24         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         3.19         0.43        22.85        14.40        19.07 
TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        0.13        38.63        14.27        12.82         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      4P LOSS CNV 4P LOSS WILD-TYPE 
             1.22              0.07 
      4P LOSS CNV 4P LOSS WILD-TYPE 
            44.68             90.67 
      4P LOSS CNV 4P LOSS WILD-TYPE 
           14.250            12.195 
[1] "1.2 - 44.7 (14.2)" "0.1 - 90.7 (12.2)"
       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 CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" "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 CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" "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 CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"       "4P LOSS CNV" "4P LOSS WILD-TYPE"       "4P LOSS CNV" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"       "4P LOSS CNV"       "4P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS CNV          3    6
  4P LOSS WILD-TYPE   22   41
        clus
vv       4P LOSS CNV 4P LOSS WILD-TYPE
  FEMALE           3                22
  MALE             6                41
                   vv
clus                M0 M1 MX
  4P LOSS CNV        6  0  3
  4P LOSS WILD-TYPE 42  1 20
D39V4, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  M0           6                42
  M1           0                 1
  MX           3                20
                   vv
clus                N0 N1 NX
  4P LOSS CNV        6  0  3
  4P LOSS WILD-TYPE 43  1 18
D39V5, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  N0           6                43
  N1           0                 1
  NX           3                18
                   vv
clus                R0 R1 R2 RX
  4P LOSS CNV        7  1  0  1
  4P LOSS WILD-TYPE 43  7  1  7
D39V6, multiclass
    clus
vv   4P LOSS CNV 4P LOSS WILD-TYPE
  R0           7                43
  R1           1                 7
  R2           0                 1
  RX           1                 7
D39V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  4P LOSS CNV             4        2          1          0          0         0
  4P LOSS WILD-TYPE      25       10         15          4          1         1
D39V8, multiclass

Clustering(40) Variable = 4q loss
D40V1, survival
                   sevent
clus2                0  1
  4Q LOSS CNV        7  6
  4Q LOSS WILD-TYPE 33 20
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
               13                53 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
                6                20 
$`4Q LOSS CNV`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A 
       27.52        23.34         5.03        55.17        53.29         2.60 
TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25X TCGA-G3-A25Y 
        6.02        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-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB 
        0.26         8.28         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
        0.13        37.74        83.57        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S 
       53.52         6.67        34.06        29.16         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        38.63        40.47        14.27        12.82 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      4Q LOSS CNV 4Q LOSS WILD-TYPE 
             1.22              0.07 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            55.17             90.67 
      4Q LOSS CNV 4Q LOSS WILD-TYPE 
            13.64             12.82 
[1] "1.2 - 55.2 (13.6)" "0.1 - 90.7 (12.8)"
       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 CNV" "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 CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "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 CNV"       "4Q LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "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 CNV"       "4Q LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"       "4Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"       "4Q LOSS CNV" "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 CNV"       "4Q LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
      "4Q LOSS CNV" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS CNV          4   11
  4Q LOSS WILD-TYPE   21   36
        clus
vv       4Q LOSS CNV 4Q LOSS WILD-TYPE
  FEMALE           4                21
  MALE            11                36
                   vv
clus                M0 M1 MX
  4Q LOSS CNV       10  0  5
  4Q LOSS WILD-TYPE 38  1 18
D40V4, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  M0          10                38
  M1           0                 1
  MX           5                18
                   vv
clus                N0 N1 NX
  4Q LOSS CNV       11  0  4
  4Q LOSS WILD-TYPE 38  1 17
D40V5, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  N0          11                38
  N1           0                 1
  NX           4                17
                   vv
clus                R0 R1 R2 RX
  4Q LOSS CNV       12  2  0  1
  4Q LOSS WILD-TYPE 38  6  1  7
D40V6, multiclass
    clus
vv   4Q LOSS CNV 4Q LOSS WILD-TYPE
  R0          12                38
  R1           2                 6
  R2           0                 1
  RX           1                 7
D40V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  4Q LOSS CNV             6        4          2          0          0         0
  4Q LOSS WILD-TYPE      23        8         14          4          1         1
D40V8, multiclass

Clustering(41) Variable = 5q loss
D41V1, survival
                   sevent
clus2                0  1
  5Q LOSS CNV        1  3
  5Q LOSS WILD-TYPE 39 23
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                4                62 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
                3                23 
$`5Q LOSS CNV`
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-CC-A3MA 
       37.61        13.81         0.26         8.28         0.07         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       44.68        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      5Q LOSS CNV 5Q LOSS WILD-TYPE 
             1.22              0.07 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            22.85             90.67 
      5Q LOSS CNV 5Q LOSS WILD-TYPE 
            7.185            13.725 
[1] "1.2 - 22.9 (7.2)"  "0.1 - 90.7 (13.7)"
       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 CNV" 
       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-CC-A3MA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" "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 CNV" 
       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-CC-A3MA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" "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 CNV" 
       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-CC-A3MA 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"       "5Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
[1] "hr=" "5.8"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS CNV          1    3
  5Q LOSS WILD-TYPE   24   44
        clus
vv       5Q LOSS CNV 5Q LOSS WILD-TYPE
  FEMALE           1                24
  MALE             3                44
                   vv
clus                M0 M1 MX
  5Q LOSS CNV        2  0  2
  5Q LOSS WILD-TYPE 46  1 21
D41V4, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  M0           2                46
  M1           0                 1
  MX           2                21
                   vv
clus                N0 N1 NX
  5Q LOSS CNV        2  0  2
  5Q LOSS WILD-TYPE 47  1 19
D41V5, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  N0           2                47
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  5Q LOSS CNV        2  1  0  1
  5Q LOSS WILD-TYPE 48  7  1  7
D41V6, multiclass
    clus
vv   5Q LOSS CNV 5Q LOSS WILD-TYPE
  R0           2                48
  R1           1                 7
  R2           0                 1
  RX           1                 7
D41V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  5Q LOSS CNV             2        0          1          0          0         0
  5Q LOSS WILD-TYPE      27       12         15          4          1         1
D41V8, multiclass

Clustering(42) Variable = 6q loss
D42V1, survival
                   sevent
clus2                0  1
  6Q LOSS CNV        9  2
  6Q LOSS WILD-TYPE 31 24
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
               11                55 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
                2                24 
$`6Q LOSS CNV`
TCGA-BC-A10Q TCGA-CC-A3MA TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1EE 
       37.32         0.07        22.78        21.44        19.76         6.67 
TCGA-EP-A12J TCGA-EP-A3RK TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25X 
        4.24         0.43        19.07        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-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        53.29 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       66.31        53.52        34.06         6.02        29.16        13.64 
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-A3R3 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40         0.13         1.22        40.47        14.27        12.82 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      6Q LOSS CNV 6Q LOSS WILD-TYPE 
             0.07              0.07 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            44.68             90.67 
      6Q LOSS CNV 6Q LOSS WILD-TYPE 
            19.76             11.57 
[1] "0.1 - 44.7 (19.8)" "0.1 - 90.7 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "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-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "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 CNV" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "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 CNV" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "6Q LOSS CNV" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"       "6Q LOSS CNV" "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 CNV" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS CNV          5    7
  6Q LOSS WILD-TYPE   20   40
        clus
vv       6Q LOSS CNV 6Q LOSS WILD-TYPE
  FEMALE           5                20
  MALE             7                40
                   vv
clus                M0 M1 MX
  6Q LOSS CNV        9  0  3
  6Q LOSS WILD-TYPE 39  1 20
D42V4, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  M0           9                39
  M1           0                 1
  MX           3                20
                   vv
clus                N0 N1 NX
  6Q LOSS CNV        9  0  3
  6Q LOSS WILD-TYPE 40  1 18
D42V5, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  N0           9                40
  N1           0                 1
  NX           3                18
                   vv
clus                R0 R1 R2 RX
  6Q LOSS CNV        7  1  0  3
  6Q LOSS WILD-TYPE 43  7  1  5
D42V6, multiclass
    clus
vv   6Q LOSS CNV 6Q LOSS WILD-TYPE
  R0           7                43
  R1           1                 7
  R2           0                 1
  RX           3                 5
D42V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  6Q LOSS CNV             5        2          3          1          0         0
  6Q LOSS WILD-TYPE      24       10         13          3          1         1
D42V8, multiclass

Clustering(43) Variable = 7p loss
D43V1, survival
                   sevent
clus2                0  1
  7P LOSS CNV        3  0
  7P LOSS WILD-TYPE 37 26
      7P LOSS CNV 7P LOSS WILD-TYPE 
                3                63 
      7P LOSS CNV 7P LOSS WILD-TYPE 
                0                26 
$`7P LOSS CNV`
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-CC-A3MA 
        5.03        37.61         0.26         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        3.65         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      7P LOSS CNV 7P LOSS WILD-TYPE 
             1.97              0.07 
      7P LOSS CNV 7P LOSS WILD-TYPE 
            13.81             90.67 
      7P LOSS CNV 7P LOSS WILD-TYPE 
             8.28             13.64 
[1] "2.0 - 13.8 (8.3)"  "0.1 - 90.7 (13.6)"
       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 CNV" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" "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 CNV" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" "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 CNV" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7P LOSS WILD-TYPE"       "7P LOSS CNV" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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-A3CH        TCGA-G3-A3CI 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
[1] "hr="     "9600000"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS CNV          4    1
  7P LOSS WILD-TYPE   21   46
        clus
vv       7P LOSS CNV 7P LOSS WILD-TYPE
  FEMALE           4                21
  MALE             1                46
                   vv
clus                M0 M1 MX
  7P LOSS CNV        3  0  2
  7P LOSS WILD-TYPE 45  1 21
D43V4, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  M0           3                45
  M1           0                 1
  MX           2                21
                   vv
clus                N0 N1 NX
  7P LOSS CNV        3  0  2
  7P LOSS WILD-TYPE 46  1 19
D43V5, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  N0           3                46
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  7P LOSS CNV        4  0  0  1
  7P LOSS WILD-TYPE 46  8  1  7
D43V6, multiclass
    clus
vv   7P LOSS CNV 7P LOSS WILD-TYPE
  R0           4                46
  R1           0                 8
  R2           0                 1
  RX           1                 7
D43V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7P LOSS CNV             1        4          0          0          0         0
  7P LOSS WILD-TYPE      28        8         16          4          1         1
D43V8, multiclass

Clustering(44) Variable = 7q loss
D44V1, survival
                   sevent
clus2                0  1
  7Q LOSS CNV        4  2
  7Q LOSS WILD-TYPE 36 24
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                6                60 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
                2                24 
$`7Q LOSS CNV`
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-CC-A3MA TCGA-CC-A3MB 
       37.61         0.26         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
        6.02        29.16         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        3.19         0.43        22.85        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         6.31         5.88         4.47         0.89 

      7Q LOSS CNV 7Q LOSS WILD-TYPE 
             1.22              0.07 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
            48.99             90.67 
      7Q LOSS CNV 7Q LOSS WILD-TYPE 
           10.960            13.545 
[1] "1.2 - 49.0 (11.0)" "0.1 - 90.7 (13.5)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "7Q LOSS CNV" "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 CNV" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "7Q LOSS CNV" "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 CNV" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "7Q LOSS CNV" "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 CNV" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"       "7Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS CNV          4    3
  7Q LOSS WILD-TYPE   21   44
        clus
vv       7Q LOSS CNV 7Q LOSS WILD-TYPE
  FEMALE           4                21
  MALE             3                44
                   vv
clus                M0 M1 MX
  7Q LOSS CNV        6  0  1
  7Q LOSS WILD-TYPE 42  1 22
D44V4, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  M0           6                42
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  7Q LOSS CNV        5  0  2
  7Q LOSS WILD-TYPE 44  1 19
D44V5, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  N0           5                44
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  7Q LOSS CNV        4  2  0  1
  7Q LOSS WILD-TYPE 46  6  1  7
D44V6, multiclass
    clus
vv   7Q LOSS CNV 7Q LOSS WILD-TYPE
  R0           4                46
  R1           2                 6
  R2           0                 1
  RX           1                 7
D44V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7Q LOSS CNV             2        4          1          0          0         0
  7Q LOSS WILD-TYPE      27        8         15          4          1         1
D44V8, multiclass

Clustering(45) Variable = 8p loss
D45V1, survival
                   sevent
clus2                0  1
  8P LOSS CNV       14 13
  8P LOSS WILD-TYPE 26 13
      8P LOSS CNV 8P LOSS WILD-TYPE 
               27                39 
      8P LOSS CNV 8P LOSS WILD-TYPE 
               13                13 
$`8P LOSS CNV`
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        55.17        83.57        53.29        22.78 
TCGA-DD-A11C TCGA-DD-A1EE TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A26S TCGA-EP-A2KA 
       21.44         6.67        29.16        13.64         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S 
        0.62         0.43        22.85        14.40        19.07         1.22 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CJ 
       12.82        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-CC-A3MA 
        1.12        69.57         0.26         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
        0.10         0.13        37.74         7.33         2.60         0.46 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       51.25        90.67        79.36        66.31        19.76        53.52 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3JL TCGA-FV-A3R3 
       34.06         6.02         4.24         1.97         3.19         0.13 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       38.63        40.47        14.27        44.68         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
        6.31         5.88         0.89 

      8P LOSS CNV 8P LOSS WILD-TYPE 
             0.43              0.07 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            83.57             90.67 
      8P LOSS CNV 8P LOSS WILD-TYPE 
            14.40              8.32 
[1] "0.4 - 83.6 (14.4)" "0.1 - 90.7 (8.3)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
      "8P LOSS CNV"       "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
      "8P LOSS CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" "8P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV"       "8P LOSS CNV" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P LOSS WILD-TYPE"       "8P LOSS CNV" "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 CNV" "8P LOSS WILD-TYPE"       "8P LOSS CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
      "8P LOSS CNV" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS CNV         13   17
  8P LOSS WILD-TYPE   12   30
        clus
vv       8P LOSS CNV 8P LOSS WILD-TYPE
  FEMALE          13                12
  MALE            17                30
                   vv
clus                M0 M1 MX
  8P LOSS CNV       19  0 11
  8P LOSS WILD-TYPE 29  1 12
D45V4, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  M0          19                29
  M1           0                 1
  MX          11                12
                   vv
clus                N0 N1 NX
  8P LOSS CNV       18  1 11
  8P LOSS WILD-TYPE 31  0 10
D45V5, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  N0          18                31
  N1           1                 0
  NX          11                10
                   vv
clus                R0 R1 R2 RX
  8P LOSS CNV       20  4  0  3
  8P LOSS WILD-TYPE 30  4  1  5
D45V6, multiclass
    clus
vv   8P LOSS CNV 8P LOSS WILD-TYPE
  R0          20                30
  R1           4                 4
  R2           0                 1
  RX           3                 5
D45V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8P LOSS CNV             9        7          7          2          1         0
  8P LOSS WILD-TYPE      20        5          9          2          0         1
D45V8, multiclass

Clustering(46) Variable = 8q loss
D46V1, survival
                   sevent
clus2                0  1
  8Q LOSS CNV        2  2
  8Q LOSS WILD-TYPE 38 24
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                4                62 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
                2                24 
$`8Q LOSS CNV`
TCGA-BC-A10T TCGA-BC-A217 TCGA-BC-A3KG TCGA-G3-A25Y 
       27.52        13.81         8.28        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-CC-A3MA TCGA-CC-A3MB 
       37.61         0.26         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       12.82        44.68         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      8Q LOSS CNV 8Q LOSS WILD-TYPE 
             8.28              0.07 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
            27.52             90.67 
      8Q LOSS CNV 8Q LOSS WILD-TYPE 
           14.335            12.195 
[1] "8.3 - 27.5 (14.3)" "0.1 - 90.7 (12.2)"
       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 CNV" "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 CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
      "8Q LOSS CNV" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        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 CNV" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
[1] "hr=" "1.9"
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS CNV          3    2
  8Q LOSS WILD-TYPE   22   45
        clus
vv       8Q LOSS CNV 8Q LOSS WILD-TYPE
  FEMALE           3                22
  MALE             2                45
                   vv
clus                M0 M1 MX
  8Q LOSS CNV        4  0  1
  8Q LOSS WILD-TYPE 44  1 22
D46V4, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  M0           4                44
  M1           0                 1
  MX           1                22
                   vv
clus                N0 N1 NX
  8Q LOSS CNV        3  0  2
  8Q LOSS WILD-TYPE 46  1 19
D46V5, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  N0           3                46
  N1           0                 1
  NX           2                19
                   vv
clus                R0 R1 R2 RX
  8Q LOSS CNV        3  1  0  1
  8Q LOSS WILD-TYPE 47  7  1  7
D46V6, multiclass
    clus
vv   8Q LOSS CNV 8Q LOSS WILD-TYPE
  R0           3                47
  R1           1                 7
  R2           0                 1
  RX           1                 7
D46V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8Q LOSS CNV             1        3          0          0          0         0
  8Q LOSS WILD-TYPE      28        9         16          4          1         1
D46V8, multiclass

Clustering(47) Variable = 9p loss
D47V1, survival
                   sevent
clus2                0  1
  9P LOSS CNV        9  7
  9P LOSS WILD-TYPE 31 19
      9P LOSS CNV 9P LOSS WILD-TYPE 
               16                50 
      9P LOSS CNV 9P LOSS WILD-TYPE 
                7                19 
$`9P LOSS CNV`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-A3MB 
       48.99        10.13        27.52         5.03         0.07         0.10 
TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       55.17        83.57        53.29         2.60         0.46        21.44 
TCGA-DD-A1EI TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T 
        6.02         0.43         1.22        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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A118 
        8.28         4.24         0.07         0.13        37.74        22.78 
TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
       53.52         6.67        34.06        29.16        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-FV-A3R3 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07         0.13        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       44.68        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      9P LOSS CNV 9P LOSS WILD-TYPE 
             0.07              0.07 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            83.57             90.67 
      9P LOSS CNV 9P LOSS WILD-TYPE 
            8.075            13.725 
[1] "0.1 - 83.6 (8.1)"  "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "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 CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "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 CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "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 CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9P LOSS CNV" "9P LOSS WILD-TYPE"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
      "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9P LOSS CNV"       "9P LOSS CNV"       "9P LOSS CNV" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"       "9P LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9P LOSS CNV" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"       "9P LOSS CNV"       "9P LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
[1] "hr=" "1"  
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS CNV          5   12
  9P LOSS WILD-TYPE   20   35
        clus
vv       9P LOSS CNV 9P LOSS WILD-TYPE
  FEMALE           5                20
  MALE            12                35
                   vv
clus                M0 M1 MX
  9P LOSS CNV       12  0  5
  9P LOSS WILD-TYPE 36  1 18
D47V4, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  M0          12                36
  M1           0                 1
  MX           5                18
                   vv
clus                N0 N1 NX
  9P LOSS CNV       13  0  4
  9P LOSS WILD-TYPE 36  1 17
D47V5, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  N0          13                36
  N1           0                 1
  NX           4                17
                   vv
clus                R0 R1 R2 RX
  9P LOSS CNV       10  3  0  3
  9P LOSS WILD-TYPE 40  5  1  5
D47V6, multiclass
    clus
vv   9P LOSS CNV 9P LOSS WILD-TYPE
  R0          10                40
  R1           3                 5
  R2           0                 1
  RX           3                 5
D47V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9P LOSS CNV             5        4          5          0          0         0
  9P LOSS WILD-TYPE      24        8         11          4          1         1
D47V8, multiclass

Clustering(48) Variable = 9q loss
D48V1, survival
                   sevent
clus2                0  1
  9Q LOSS CNV        9  5
  9Q LOSS WILD-TYPE 31 21
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
               14                52 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
                5                21 
$`9Q LOSS CNV`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-CC-A3MB TCGA-DD-A113 
       10.13        27.52         5.03         0.07         0.10        55.17 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EI TCGA-EP-A3RK 
       53.29         2.60         0.46        21.44         6.02         0.43 
TCGA-G3-A25S TCGA-G3-A25T 
        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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 
        0.26         8.28         4.24         0.07         0.13        37.74 
TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       83.57        22.78         7.33        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EJ 
       66.31        19.76        53.52         6.67        34.06        29.16 
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-FV-A3R3 TCGA-G3-A25U 
        3.19        22.85        14.40        19.07         0.13        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      9Q LOSS CNV 9Q LOSS WILD-TYPE 
             0.07              0.07 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            55.17             90.67 
      9Q LOSS CNV 9Q LOSS WILD-TYPE 
            5.525            14.040 
[1] "0.1 - 55.2 (5.5)"  "0.1 - 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 CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9Q LOSS CNV"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" "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 CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9Q LOSS CNV"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" "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 CNV" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "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 CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-CC-A3MA 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-CC-A3MB        TCGA-CC-A3MC        TCGA-DD-A113        TCGA-DD-A114 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D 
      "9Q LOSS CNV"       "9Q LOSS CNV"       "9Q LOSS CNV" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"       "9Q LOSS CNV" 
       TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR 
      "9Q LOSS CNV" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A3R3        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"       "9Q LOSS CNV"       "9Q LOSS CNV" "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-A3CH        TCGA-G3-A3CI 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS CNV          4   11
  9Q LOSS WILD-TYPE   21   36
        clus
vv       9Q LOSS CNV 9Q LOSS WILD-TYPE
  FEMALE           4                21
  MALE            11                36
                   vv
clus                M0 M1 MX
  9Q LOSS CNV       10  0  5
  9Q LOSS WILD-TYPE 38  1 18
D48V4, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  M0          10                38
  M1           0                 1
  MX           5                18
                   vv
clus                N0 N1 NX
  9Q LOSS CNV       11  0  4
  9Q LOSS WILD-TYPE 38  1 17
D48V5, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  N0          11                38
  N1           0                 1
  NX           4                17
                   vv
clus                R0 R1 R2 RX
  9Q LOSS CNV        9  2  0  3
  9Q LOSS WILD-TYPE 41  6  1  5
D48V6, multiclass
    clus
vv   9Q LOSS CNV 9Q LOSS WILD-TYPE
  R0           9                41
  R1           2                 6
  R2           0                 1
  RX           3                 5
D48V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9Q LOSS CNV             5        4          3          0          0         0
  9Q LOSS WILD-TYPE      24        8         13          4          1         1
D48V8, multiclass

Clustering(49) Variable = 10p loss
D49V1, survival
                    sevent
clus2                 0  1
  10P LOSS CNV        2  1
  10P LOSS WILD-TYPE 38 25
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 3                 63 
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 1                 25 
$`10P LOSS CNV`
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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 
        0.10         0.13        55.17        37.74        83.57        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 
       22.78         7.33         2.60         0.46        51.25        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      10P LOSS CNV 10P LOSS WILD-TYPE 
              5.03               0.07 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             21.44              90.67 
      10P LOSS CNV 10P LOSS WILD-TYPE 
             11.57              13.64 
[1] "5.0 - 21.4 (11.6)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"       "10P LOSS CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS CNV          0    3
  10P LOSS WILD-TYPE   25   44
        clus
vv       10P LOSS CNV 10P LOSS WILD-TYPE
  FEMALE            0                 25
  MALE              3                 44
                    vv
clus                 M0 M1 MX
  10P LOSS CNV        1  0  2
  10P LOSS WILD-TYPE 47  1 21
D49V4, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  M0            1                 47
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  10P LOSS CNV        2  0  1
  10P LOSS WILD-TYPE 47  1 20
D49V5, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  10P LOSS CNV        1  1  0  1
  10P LOSS WILD-TYPE 49  7  1  7
D49V6, multiclass
    clus
vv   10P LOSS CNV 10P LOSS WILD-TYPE
  R0            1                 49
  R1            1                  7
  R2            0                  1
  RX            1                  7
D49V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS CNV             1        0          1          0          0
  10P LOSS WILD-TYPE      28       12         15          4          1
                    vv
clus                 STAGE IVB
  10P LOSS CNV               0
  10P LOSS WILD-TYPE         1
D49V8, multiclass
[1] "Remove cluster labels:" "10P LOSS CNV"          
clus
      10P LOSS CNV 10P LOSS WILD-TYPE 
                 2                 61 
        TCGA-BC-4072         TCGA-BC-A10X         TCGA-BC-A10Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A216         TCGA-BC-A217         TCGA-BC-A3KF 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-CC-5258         TCGA-CC-5260 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5261         TCGA-CC-5262         TCGA-CC-5263 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5264         TCGA-CC-A1HT         TCGA-CC-A3MA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-A3MB         TCGA-CC-A3MC         TCGA-DD-A113 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A114         TCGA-DD-A115         TCGA-DD-A116 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A118         TCGA-DD-A119         TCGA-DD-A11A 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11B         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I1         TCGA-FV-A3R3 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" 

Clustering(50) Variable = 10q loss
D50V1, survival
                    sevent
clus2                 0  1
  10Q LOSS CNV        6  5
  10Q LOSS WILD-TYPE 34 21
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                11                 55 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
                 5                 21 
$`10Q LOSS CNV`
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-CC-A3MA TCGA-DD-A11C TCGA-DD-A1EL TCGA-G3-A25U TCGA-G3-A25X 
        0.07        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-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        4.24         0.10         0.13        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D 
       53.29        22.78         7.33         2.60         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06         6.02        29.16         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13         1.22        38.63        14.27        12.82 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      10Q LOSS CNV 10Q LOSS WILD-TYPE 
              0.07               0.07 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             44.68              90.67 
      10Q LOSS CNV 10Q LOSS WILD-TYPE 
             13.64              12.82 
[1] "0.1 - 44.7 (13.6)" "0.1 - 90.7 (12.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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 CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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 CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV"       "10Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "10Q LOSS CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "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 CNV" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE"       "10Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"10Q LOSS WILD-TYPE"       "10Q LOSS CNV" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS CNV          5    8
  10Q LOSS WILD-TYPE   20   39
        clus
vv       10Q LOSS CNV 10Q LOSS WILD-TYPE
  FEMALE            5                 20
  MALE              8                 39
                    vv
clus                 M0 M1 MX
  10Q LOSS CNV        8  0  5
  10Q LOSS WILD-TYPE 40  1 18
D50V4, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  M0            8                 40
  M1            0                  1
  MX            5                 18
                    vv
clus                 N0 N1 NX
  10Q LOSS CNV        8  0  5
  10Q LOSS WILD-TYPE 41  1 16
D50V5, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  N0            8                 41
  N1            0                  1
  NX            5                 16
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS CNV        7  3  0  2
  10Q LOSS WILD-TYPE 43  5  1  6
D50V6, multiclass
    clus
vv   10Q LOSS CNV 10Q LOSS WILD-TYPE
  R0            7                 43
  R1            3                  5
  R2            0                  1
  RX            2                  6
D50V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS CNV             2        3          3          1          0
  10Q LOSS WILD-TYPE      27        9         13          3          1
                    vv
clus                 STAGE IVB
  10Q LOSS CNV               0
  10Q LOSS WILD-TYPE         1
D50V8, multiclass

Clustering(51) Variable = 11p loss
D51V1, survival
                    sevent
clus2                 0  1
  11P LOSS CNV        3  3
  11P LOSS WILD-TYPE 37 23
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 6                 60 
      11P LOSS CNV 11P LOSS WILD-TYPE 
                 3                 23 
$`11P LOSS CNV`
TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 
       37.32         5.03        13.81         0.07        55.17        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-CC-A3MB TCGA-CC-A3MC 
        0.26         8.28         0.07         4.24         0.10         0.13 
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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        0.43        22.85        14.40        19.07         0.13         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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.84         8.32         6.31         5.88         4.47         0.89 

      11P LOSS CNV 11P LOSS WILD-TYPE 
              0.07               0.07 
      11P LOSS CNV 11P LOSS WILD-TYPE 
             83.57              90.67 
      11P LOSS CNV 11P LOSS WILD-TYPE 
            25.565             12.195 
[1] "0.1 - 83.6 (25.6)" "0.1 - 90.7 (12.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        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 CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "11P LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "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 CNV" 
        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 CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "11P LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "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 CNV" 
        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 CNV" "11P LOSS WILD-TYPE"       "11P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"       "11P LOSS CNV" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "11P LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS CNV          3    3
  11P LOSS WILD-TYPE   22   44
        clus
vv       11P LOSS CNV 11P LOSS WILD-TYPE
  FEMALE            3                 22
  MALE              3                 44
                    vv
clus                 M0 M1 MX
  11P LOSS CNV        4  0  2
  11P LOSS WILD-TYPE 44  1 21
D51V4, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  M0            4                 44
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  11P LOSS CNV        3  0  3
  11P LOSS WILD-TYPE 46  1 18
D51V5, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  N0            3                 46
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  11P LOSS CNV        5  1  0  0
  11P LOSS WILD-TYPE 45  7  1  8
D51V6, multiclass
    clus
vv   11P LOSS CNV 11P LOSS WILD-TYPE
  R0            5                 45
  R1            1                  7
  R2            0                  1
  RX            0                  8
D51V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS CNV             0        2          2          0          0
  11P LOSS WILD-TYPE      29       10         14          4          1
                    vv
clus                 STAGE IVB
  11P LOSS CNV               0
  11P LOSS WILD-TYPE         1
D51V8, multiclass

Clustering(52) Variable = 11q loss
D52V1, survival
                    sevent
clus2                 0  1
  11Q LOSS CNV        4  3
  11Q LOSS WILD-TYPE 36 23
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 7                 59 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
                 3                 23 
$`11Q LOSS CNV`
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        55.17 
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 
        8.28         0.07         0.07         0.10         0.13        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-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         0.13        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      11Q LOSS CNV 11Q LOSS WILD-TYPE 
              1.22               0.07 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             55.17              90.67 
      11Q LOSS CNV 11Q LOSS WILD-TYPE 
             11.57              13.64 
[1] "1.2 - 55.2 (11.6)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        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 CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-A3CH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        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 CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-A3CH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV"       "11Q LOSS CNV" 
        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 CNV" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
      "11Q LOSS CNV" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"11Q LOSS WILD-TYPE"       "11Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE"       "11Q LOSS CNV" 
        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-A3CH 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS CNV          3    5
  11Q LOSS WILD-TYPE   22   42
        clus
vv       11Q LOSS CNV 11Q LOSS WILD-TYPE
  FEMALE            3                 22
  MALE              5                 42
                    vv
clus                 M0 M1 MX
  11Q LOSS CNV        5  0  3
  11Q LOSS WILD-TYPE 43  1 20
D52V4, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  M0            5                 43
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  11Q LOSS CNV        5  0  3
  11Q LOSS WILD-TYPE 44  1 18
D52V5, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  N0            5                 44
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS CNV        3  3  0  2
  11Q LOSS WILD-TYPE 47  5  1  6
D52V6, multiclass
    clus
vv   11Q LOSS CNV 11Q LOSS WILD-TYPE
  R0            3                 47
  R1            3                  5
  R2            0                  1
  RX            2                  6
D52V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS CNV             1        2          3          0          0
  11Q LOSS WILD-TYPE      28       10         13          4          1
                    vv
clus                 STAGE IVB
  11Q LOSS CNV               0
  11Q LOSS WILD-TYPE         1
D52V8, multiclass

Clustering(53) Variable = 12p loss
D53V1, survival
                    sevent
clus2                 0  1
  12P LOSS CNV        5  0
  12P LOSS WILD-TYPE 35 26
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 5                 61 
      12P LOSS CNV 12P LOSS WILD-TYPE 
                 0                 26 
$`12P LOSS CNV`
TCGA-BC-A217 TCGA-DD-A1EC TCGA-DD-A1EJ TCGA-G3-A25S TCGA-G3-A25Z 
       13.81        19.76        29.16         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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        90.67        79.36        66.31        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06         6.02        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      12P LOSS CNV 12P LOSS WILD-TYPE 
              1.22               0.07 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             29.16              90.67 
      12P LOSS CNV 12P LOSS WILD-TYPE 
             13.81              12.82 
[1] "1.2 - 29.2 (13.8)" "0.1 - 90.7 (12.8)"
        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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        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-A3CH 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        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-A3CH 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12P LOSS WILD-TYPE"       "12P LOSS CNV" "12P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"       "12P LOSS CNV" 
        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-A3CH 
      "12P LOSS CNV" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr="     "7.5e+07"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS CNV          3    2
  12P LOSS WILD-TYPE   22   45
        clus
vv       12P LOSS CNV 12P LOSS WILD-TYPE
  FEMALE            3                 22
  MALE              2                 45
                    vv
clus                 M0 M1 MX
  12P LOSS CNV        5  0  0
  12P LOSS WILD-TYPE 43  1 23
D53V4, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  M0            5                 43
  M1            0                  1
  MX            0                 23
                    vv
clus                 N0 N1 NX
  12P LOSS CNV        3  1  1
  12P LOSS WILD-TYPE 46  0 20
D53V5, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  N0            3                 46
  N1            1                  0
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  12P LOSS CNV        4  1  0  0
  12P LOSS WILD-TYPE 46  7  1  8
D53V6, multiclass
    clus
vv   12P LOSS CNV 12P LOSS WILD-TYPE
  R0            4                 46
  R1            1                  7
  R2            0                  1
  RX            0                  8
D53V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  12P LOSS CNV             3        1          0          0          1
  12P LOSS WILD-TYPE      26       11         16          4          0
                    vv
clus                 STAGE IVB
  12P LOSS CNV               0
  12P LOSS WILD-TYPE         1
D53V8, multiclass

Clustering(54) Variable = 12q loss
D54V1, survival
                    sevent
clus2                 0  1
  12Q LOSS CNV        3  0
  12Q LOSS WILD-TYPE 37 26
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 3                 63 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
                 0                 26 
$`12Q LOSS CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        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-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE 
       51.25        90.67        79.36        66.31        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.65         1.97         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       14.40        19.07         0.13         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH 
       14.27        12.82        44.68        14.86         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      12Q LOSS CNV 12Q LOSS WILD-TYPE 
              8.84               0.07 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
             19.76              90.67 
      12Q LOSS CNV 12Q LOSS WILD-TYPE 
             13.81              12.82 
[1] "8.8 - 19.8 (13.8)" "0.1 - 90.7 (12.8)"
        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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE"       "12Q LOSS CNV" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "12Q LOSS CNV" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
[1] "hr="     "2.6e+07"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS CNV          2    1
  12Q LOSS WILD-TYPE   23   46
        clus
vv       12Q LOSS CNV 12Q LOSS WILD-TYPE
  FEMALE            2                 23
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  12Q LOSS CNV        3  0  0
  12Q LOSS WILD-TYPE 45  1 23
D54V4, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  M0            3                 45
  M1            0                  1
  MX            0                 23
                    vv
clus                 N0 N1 NX
  12Q LOSS CNV        2  0  1
  12Q LOSS WILD-TYPE 47  1 20
D54V5, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  12Q LOSS CNV        3  0  0  0
  12Q LOSS WILD-TYPE 47  8  1  8
D54V6, multiclass
    clus
vv   12Q LOSS CNV 12Q LOSS WILD-TYPE
  R0            3                 47
  R1            0                  8
  R2            0                  1
  RX            0                  8
D54V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  12Q LOSS CNV             2        1          0          0          0
  12Q LOSS WILD-TYPE      27       11         16          4          1
                    vv
clus                 STAGE IVB
  12Q LOSS CNV               0
  12Q LOSS WILD-TYPE         1
D54V8, multiclass

Clustering(55) Variable = 13q loss
D55V1, survival
                    sevent
clus2                 0  1
  13Q LOSS CNV       14  6
  13Q LOSS WILD-TYPE 26 20
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                20                 46 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
                 6                 20 
$`13Q LOSS CNV`
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-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.07         0.07        55.17        83.57        53.29        22.78 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EI TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T 
        2.60        21.44         6.02         0.43         1.22        38.63 
TCGA-G3-A25X TCGA-G3-A3CH 
       44.68         6.31 

$`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-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
        0.10         0.13        37.74         7.33         0.46        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06        29.16        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-FV-A3R3 TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
        0.13        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 

      13Q LOSS CNV 13Q LOSS WILD-TYPE 
              0.07               0.10 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             83.57              90.67 
      13Q LOSS CNV 13Q LOSS WILD-TYPE 
             11.97              13.23 
[1] "0.1 - 83.6 (12.0)" "0.1 - 90.7 (13.2)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        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 CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        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 CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        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 CNV" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "13Q LOSS CNV"       "13Q LOSS CNV"       "13Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "13Q LOSS CNV" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"13Q LOSS WILD-TYPE"       "13Q LOSS CNV" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"       "13Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS CNV          8   16
  13Q LOSS WILD-TYPE   17   31
        clus
vv       13Q LOSS CNV 13Q LOSS WILD-TYPE
  FEMALE            8                 17
  MALE             16                 31
                    vv
clus                 M0 M1 MX
  13Q LOSS CNV       19  0  5
  13Q LOSS WILD-TYPE 29  1 18
D55V4, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  M0           19                 29
  M1            0                  1
  MX            5                 18
                    vv
clus                 N0 N1 NX
  13Q LOSS CNV       18  0  6
  13Q LOSS WILD-TYPE 31  1 15
D55V5, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  N0           18                 31
  N1            0                  1
  NX            6                 15
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS CNV       14  3  0  5
  13Q LOSS WILD-TYPE 36  5  1  3
D55V6, multiclass
    clus
vv   13Q LOSS CNV 13Q LOSS WILD-TYPE
  R0           14                 36
  R1            3                  5
  R2            0                  1
  RX            5                  3
D55V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS CNV             5        7          6          2          0
  13Q LOSS WILD-TYPE      24        5         10          2          1
                    vv
clus                 STAGE IVB
  13Q LOSS CNV               0
  13Q LOSS WILD-TYPE         1
D55V8, multiclass

Clustering(56) Variable = 14q loss
D56V1, survival
                    sevent
clus2                 0  1
  14Q LOSS CNV       15  6
  14Q LOSS WILD-TYPE 25 20
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                21                 45 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
                 6                 20 
$`14Q LOSS CNV`
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-CC-A3MA TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A118 
        8.28         0.07         0.07         0.10        55.17        22.78 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A2KB 
        2.60        21.44        90.67        29.16        13.64         1.97 
TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A3CH 
        0.43         1.22         6.31 

$`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-CC-A3MC 
       23.34         1.12        69.57        37.61         4.24         0.13 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D 
       37.74        83.57        53.29         7.33         0.46        51.25 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       79.36        66.31        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
        6.02         4.24         3.62         3.65         0.62         3.19 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         0.13        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 

      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              0.07               0.13 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
             90.67              83.57 
      14Q LOSS CNV 14Q LOSS WILD-TYPE 
              8.28              14.40 
[1] "0.1 - 90.7 (8.3)"  "0.1 - 83.6 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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 CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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-A3CH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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 CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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-A3CH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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 CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "14Q LOSS CNV"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"14Q LOSS WILD-TYPE"       "14Q LOSS CNV"       "14Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "14Q LOSS CNV" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        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-A3CH 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"       "14Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS CNV          9   15
  14Q LOSS WILD-TYPE   16   32
        clus
vv       14Q LOSS CNV 14Q LOSS WILD-TYPE
  FEMALE            9                 16
  MALE             15                 32
                    vv
clus                 M0 M1 MX
  14Q LOSS CNV       18  0  6
  14Q LOSS WILD-TYPE 30  1 17
D56V4, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  M0           18                 30
  M1            0                  1
  MX            6                 17
                    vv
clus                 N0 N1 NX
  14Q LOSS CNV       15  1  8
  14Q LOSS WILD-TYPE 34  0 13
D56V5, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  N0           15                 34
  N1            1                  0
  NX            8                 13
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS CNV       15  3  0  4
  14Q LOSS WILD-TYPE 35  5  1  4
D56V6, multiclass
    clus
vv   14Q LOSS CNV 14Q LOSS WILD-TYPE
  R0           15                 35
  R1            3                  5
  R2            0                  1
  RX            4                  4
D56V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS CNV             7        6          6          0          1
  14Q LOSS WILD-TYPE      22        6         10          4          0
                    vv
clus                 STAGE IVB
  14Q LOSS CNV               0
  14Q LOSS WILD-TYPE         1
D56V8, multiclass

Clustering(57) Variable = 15q loss
D57V1, survival
                    sevent
clus2                 0  1
  15Q LOSS CNV        4  3
  15Q LOSS WILD-TYPE 36 23
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 7                 59 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
                 3                 23 
$`15Q LOSS CNV`
TCGA-BC-A112 TCGA-CC-A3MA TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A2KB 
        5.03         0.07        55.17        83.57        13.64         1.97 
TCGA-G3-A25Z 
        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-CC-A3MB TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.10         0.13        37.74        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        2.60         0.46        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       29.16         4.24         3.62         3.65         0.62         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S 
        0.43        22.85        14.40        19.07         0.13         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-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              0.07               0.07 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
             83.57              90.67 
      15Q LOSS CNV 15Q LOSS WILD-TYPE 
              8.84              13.81 
[1] "0.1 - 83.6 (8.8)"  "0.1 - 90.7 (13.8)"
        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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "15Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "15Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"       "15Q LOSS CNV" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "15Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"       "15Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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-A3CH 
      "15Q LOSS CNV" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS CNV          2    6
  15Q LOSS WILD-TYPE   23   41
        clus
vv       15Q LOSS CNV 15Q LOSS WILD-TYPE
  FEMALE            2                 23
  MALE              6                 41
                    vv
clus                 M0 M1 MX
  15Q LOSS CNV        6  0  2
  15Q LOSS WILD-TYPE 42  1 21
D57V4, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  M0            6                 42
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  15Q LOSS CNV        6  0  2
  15Q LOSS WILD-TYPE 43  1 19
D57V5, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  N0            6                 43
  N1            0                  1
  NX            2                 19
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS CNV        7  0  0  1
  15Q LOSS WILD-TYPE 43  8  1  7
D57V6, multiclass
    clus
vv   15Q LOSS CNV 15Q LOSS WILD-TYPE
  R0            7                 43
  R1            0                  8
  R2            0                  1
  RX            1                  7
D57V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS CNV             2        2          3          0          0
  15Q LOSS WILD-TYPE      27       10         13          4          1
                    vv
clus                 STAGE IVB
  15Q LOSS CNV               0
  15Q LOSS WILD-TYPE         1
D57V8, multiclass

Clustering(58) Variable = 16p loss
D58V1, survival
                    sevent
clus2                 0  1
  16P LOSS CNV        8  3
  16P LOSS WILD-TYPE 32 23
      16P LOSS CNV 16P LOSS WILD-TYPE 
                11                 55 
      16P LOSS CNV 16P LOSS WILD-TYPE 
                 3                 23 
$`16P LOSS CNV`
TCGA-BC-A217 TCGA-CC-5258 TCGA-CC-A3MC TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A1EI 
       13.81         0.07         0.13         0.46        34.06         6.02 
TCGA-DD-A1EJ TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25X TCGA-G3-A25Y 
       29.16         1.97        22.85        44.68        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-CC-A3MA 
        5.03        37.61         0.26         8.28         4.24         0.07 
TCGA-CC-A3MB TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.10        55.17        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL TCGA-EP-A12J 
       66.31        19.76        53.52         6.67        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.62         3.65         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       12.82         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

      16P LOSS CNV 16P LOSS WILD-TYPE 
              0.07               0.07 
      16P LOSS CNV 16P LOSS WILD-TYPE 
             44.68              90.67 
      16P LOSS CNV 16P LOSS WILD-TYPE 
             13.81              12.82 
[1] "0.1 - 44.7 (13.8)" "0.1 - 90.7 (12.8)"
        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 CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16P LOSS CNV" "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 CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV"       "16P LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16P LOSS CNV" "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 CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV"       "16P LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16P LOSS CNV" "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 CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"       "16P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16P LOSS CNV"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16P LOSS CNV" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"       "16P LOSS CNV" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV"       "16P LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS CNV          5   10
  16P LOSS WILD-TYPE   20   37
        clus
vv       16P LOSS CNV 16P LOSS WILD-TYPE
  FEMALE            5                 20
  MALE             10                 37
                    vv
clus                 M0 M1 MX
  16P LOSS CNV       13  0  2
  16P LOSS WILD-TYPE 35  1 21
D58V4, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  M0           13                 35
  M1            0                  1
  MX            2                 21
                    vv
clus                 N0 N1 NX
  16P LOSS CNV       11  1  3
  16P LOSS WILD-TYPE 38  0 18
D58V5, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  N0           11                 38
  N1            1                  0
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  16P LOSS CNV        9  0  0  5
  16P LOSS WILD-TYPE 41  8  1  3
D58V6, multiclass
    clus
vv   16P LOSS CNV 16P LOSS WILD-TYPE
  R0            9                 41
  R1            0                  8
  R2            0                  1
  RX            5                  3
D58V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS CNV             5        4          2          3          1
  16P LOSS WILD-TYPE      24        8         14          1          0
                    vv
clus                 STAGE IVB
  16P LOSS CNV               0
  16P LOSS WILD-TYPE         1
D58V8, multiclass

Clustering(59) Variable = 16q loss
D59V1, survival
                    sevent
clus2                 0  1
  16Q LOSS CNV       14  7
  16Q LOSS WILD-TYPE 26 19
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                21                 45 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
                 7                 19 
$`16Q LOSS CNV`
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-CC-A3MC TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B 
        4.24         0.13        55.17        53.29         2.60         0.46 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25U 
       34.06         6.02        29.16         1.97        22.85        40.47 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       44.68        14.86         6.31 

$`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-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 
        0.07         0.10        37.74        83.57        22.78         7.33 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       53.52         6.67        13.64         4.24         3.62         3.65 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        0.62         3.19         0.43        14.40        19.07         0.13 
TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        1.22        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 

      16Q LOSS CNV 16Q LOSS WILD-TYPE 
              0.07               0.07 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             55.17              90.67 
      16Q LOSS CNV 16Q LOSS WILD-TYPE 
             13.81              12.82 
[1] "0.1 - 55.2 (13.8)" "0.1 - 90.7 (12.8)"
        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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "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 CNV"       "16Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "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 CNV"       "16Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "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 CNV"       "16Q LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "16Q LOSS CNV"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "16Q LOSS CNV" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         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 CNV" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"16Q LOSS WILD-TYPE"       "16Q LOSS CNV"       "16Q LOSS CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE"       "16Q LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS CNV          9   14
  16Q LOSS WILD-TYPE   16   33
        clus
vv       16Q LOSS CNV 16Q LOSS WILD-TYPE
  FEMALE            9                 16
  MALE             14                 33
                    vv
clus                 M0 M1 MX
  16Q LOSS CNV       19  0  4
  16Q LOSS WILD-TYPE 29  1 19
D59V4, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  M0           19                 29
  M1            0                  1
  MX            4                 19
                    vv
clus                 N0 N1 NX
  16Q LOSS CNV       16  1  6
  16Q LOSS WILD-TYPE 33  0 15
D59V5, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  N0           16                 33
  N1            1                  0
  NX            6                 15
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS CNV       17  1  0  5
  16Q LOSS WILD-TYPE 33  7  1  3
D59V6, multiclass
    clus
vv   16Q LOSS CNV 16Q LOSS WILD-TYPE
  R0           17                 33
  R1            1                  7
  R2            0                  1
  RX            5                  3
D59V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS CNV             7        6          5          2          1
  16Q LOSS WILD-TYPE      22        6         11          2          0
                    vv
clus                 STAGE IVB
  16Q LOSS CNV               0
  16Q LOSS WILD-TYPE         1
D59V8, multiclass

Clustering(60) Variable = 17p loss
D60V1, survival
                    sevent
clus2                 0  1
  17P LOSS CNV       16 12
  17P LOSS WILD-TYPE 24 14
      17P LOSS CNV 17P LOSS WILD-TYPE 
                28                 38 
      17P LOSS CNV 17P LOSS WILD-TYPE 
                12                 14 
$`17P LOSS CNV`
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-CC-A3MB TCGA-CC-A3MC TCGA-DD-A115 
        8.28         0.07         4.24         0.10         0.13        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       53.29        22.78         7.33         2.60        21.44        51.25 
TCGA-DD-A1EB TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A2KC TCGA-FV-A2QR 
       66.31        34.06        29.16        13.64         0.62        19.07 
TCGA-G3-A25S TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH 
        1.22        14.86         8.84         6.31 

$`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-CC-A3MA TCGA-DD-A113 
       23.34        69.57         5.03        37.61         0.07        55.17 
TCGA-DD-A114 TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED 
       37.74         0.46        90.67        79.36        19.76        53.52 
TCGA-DD-A1EE TCGA-DD-A1EI TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
        6.67         6.02         4.24         3.62         3.65         1.97 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A3R3 TCGA-G3-A25T 
        3.19         0.43        22.85        14.40         0.13        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CI 
       40.47        14.27        12.82        44.68         8.32         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      17P LOSS CNV 17P LOSS WILD-TYPE 
              0.07               0.07 
      17P LOSS CNV 17P LOSS WILD-TYPE 
             83.57              90.67 
      17P LOSS CNV 17P LOSS WILD-TYPE 
            10.850             14.335 
[1] "0.1 - 83.6 (10.9)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        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 CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        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 CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
      "17P LOSS CNV" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
      "17P LOSS CNV"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
      "17P LOSS CNV"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV"       "17P LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17P LOSS WILD-TYPE"       "17P LOSS CNV" "17P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        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 CNV" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
      "17P LOSS CNV" "17P LOSS WILD-TYPE"       "17P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS CNV         10   20
  17P LOSS WILD-TYPE   15   27
        clus
vv       17P LOSS CNV 17P LOSS WILD-TYPE
  FEMALE           10                 15
  MALE             20                 27
                    vv
clus                 M0 M1 MX
  17P LOSS CNV       24  1  5
  17P LOSS WILD-TYPE 24  0 18
D60V4, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  M0           24                 24
  M1            1                  0
  MX            5                 18
                    vv
clus                 N0 N1 NX
  17P LOSS CNV       24  1  5
  17P LOSS WILD-TYPE 25  0 16
D60V5, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  N0           24                 25
  N1            1                  0
  NX            5                 16
                    vv
clus                 R0 R1 R2 RX
  17P LOSS CNV       20  3  1  5
  17P LOSS WILD-TYPE 30  5  0  3
D60V6, multiclass
    clus
vv   17P LOSS CNV 17P LOSS WILD-TYPE
  R0           20                 30
  R1            3                  5
  R2            1                  0
  RX            5                  3
D60V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS CNV            12        4          8          2          1
  17P LOSS WILD-TYPE      17        8          8          2          0
                    vv
clus                 STAGE IVB
  17P LOSS CNV               1
  17P LOSS WILD-TYPE         0
D60V8, multiclass

Clustering(61) Variable = 17q loss
D61V1, survival
                    sevent
clus2                 0  1
  17Q LOSS CNV        1  2
  17Q LOSS WILD-TYPE 39 24
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 3                 63 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                 24 
$`17Q LOSS CNV`
TCGA-BC-A10R TCGA-DD-A116 TCGA-DD-A1EB 
       10.13        53.29        66.31 

$`17Q 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-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        37.74        83.57 
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-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       90.67        79.36        19.76        53.52         6.67        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
        6.02        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       19.07         0.13         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-A3CH 
       12.82        44.68        14.86         8.84         8.32         6.31 
TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        5.88         4.47         0.89 

      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             10.13               0.07 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             66.31              90.67 
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
             53.29              12.82 
[1] "10.1 - 66.3 (53.3)" "0.1 - 90.7 (12.8)" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
      "17Q LOSS CNV" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-A3MA         TCGA-CC-A3MB 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE"       "17Q LOSS CNV" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25W         TCGA-G3-A25X         TCGA-G3-A25Y 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Z         TCGA-G3-A3CG         TCGA-G3-A3CH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS CNV          2    1
  17Q LOSS WILD-TYPE   23   46
        clus
vv       17Q LOSS CNV 17Q LOSS WILD-TYPE
  FEMALE            2                 23
  MALE              1                 46
                    vv
clus                 M0 M1 MX
  17Q LOSS CNV        2  0  1
  17Q LOSS WILD-TYPE 46  1 22
D61V4, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  M0            2                 46
  M1            0                  1
  MX            1                 22
                    vv
clus                 N0 N1 NX
  17Q LOSS CNV        2  0  1
  17Q LOSS WILD-TYPE 47  1 20
D61V5, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  N0            2                 47
  N1            0                  1
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS CNV        3  0  0  0
  17Q LOSS WILD-TYPE 47  8  1  8
D61V6, multiclass
    clus
vv   17Q LOSS CNV 17Q LOSS WILD-TYPE
  R0            3                 47
  R1            0                  8
  R2            0                  1
  RX            0                  8
D61V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS CNV             1        0          1          0          0
  17Q LOSS WILD-TYPE      28       12         15          4          1
                    vv
clus                 STAGE IVB
  17Q LOSS CNV               0
  17Q LOSS WILD-TYPE         1
D61V8, multiclass
[1] "Remove cluster labels:" "17Q LOSS CNV"          
clus
      17Q LOSS CNV 17Q LOSS WILD-TYPE 
                 2                 61 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A10Z         TCGA-BC-A216         TCGA-BC-A217 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5260         TCGA-CC-5261         TCGA-CC-5262 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-CC-5264         TCGA-CC-A1HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-CC-A3MA         TCGA-CC-A3MB         TCGA-CC-A3MC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A118         TCGA-DD-A119         TCGA-DD-A11A 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A11B         TCGA-DD-A11C         TCGA-DD-A11D 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1E9         TCGA-DD-A1EA         TCGA-DD-A1EC 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3I1         TCGA-FV-A3R3 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CK 
"17Q LOSS WILD-TYPE" 

Clustering(62) Variable = 18p loss
D62V1, survival
                    sevent
clus2                 0  1
  18P LOSS CNV        4  4
  18P LOSS WILD-TYPE 36 22
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 8                 58 
      18P LOSS CNV 18P LOSS WILD-TYPE 
                 4                 22 
$`18P LOSS CNV`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 TCGA-DD-A11B 
       10.13         5.03        13.81         0.10        22.78         0.46 
TCGA-ES-A2HS TCGA-G3-A25S 
       22.85         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-CC-A3MA TCGA-CC-A3MC 
        0.26         8.28         0.07         4.24         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
       55.17        37.74        83.57        53.29         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
       21.44        51.25        90.67        79.36        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL 
       53.52         6.67        34.06         6.02        29.16        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-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U 
        0.43        14.40        19.07         0.13        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

      18P LOSS CNV 18P LOSS WILD-TYPE 
              0.10               0.07 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             22.85              90.67 
      18P LOSS CNV 18P LOSS WILD-TYPE 
             7.580             13.955 
[1] "0.1 - 22.9 (7.6)"  "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 CNV" "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 CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-A3CH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "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 CNV" "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 CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-A3CH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "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 CNV" "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 CNV" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18P LOSS WILD-TYPE"       "18P LOSS CNV" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"       "18P LOSS CNV" 
        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-A3CH 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "4.5"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS CNV          3    5
  18P LOSS WILD-TYPE   22   42
        clus
vv       18P LOSS CNV 18P LOSS WILD-TYPE
  FEMALE            3                 22
  MALE              5                 42
                    vv
clus                 M0 M1 MX
  18P LOSS CNV        5  0  3
  18P LOSS WILD-TYPE 43  1 20
D62V4, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  M0            5                 43
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  18P LOSS CNV        4  0  4
  18P LOSS WILD-TYPE 45  1 17
D62V5, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  N0            4                 45
  N1            0                  1
  NX            4                 17
                    vv
clus                 R0 R1 R2 RX
  18P LOSS CNV        6  1  0  1
  18P LOSS WILD-TYPE 44  7  1  7
D62V6, multiclass
    clus
vv   18P LOSS CNV 18P LOSS WILD-TYPE
  R0            6                 44
  R1            1                  7
  R2            0                  1
  RX            1                  7
D62V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18P LOSS CNV             4        1          1          0          0
  18P LOSS WILD-TYPE      25       11         15          4          1
                    vv
clus                 STAGE IVB
  18P LOSS CNV               0
  18P LOSS WILD-TYPE         1
D62V8, multiclass

Clustering(63) Variable = 18q loss
D63V1, survival
                    sevent
clus2                 0  1
  18Q LOSS CNV        6  4
  18Q LOSS WILD-TYPE 34 22
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                10                 56 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
                 4                 22 
$`18Q LOSS CNV`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-CC-A3MB TCGA-DD-A118 
       10.13         5.03        37.61        13.81         0.10        22.78 
TCGA-DD-A11A TCGA-DD-A11B TCGA-ES-A2HS TCGA-G3-A25S 
        2.60         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-CC-A3MA TCGA-CC-A3MC TCGA-DD-A113 
        8.28         0.07         4.24         0.07         0.13        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.74        83.57        53.29         7.33        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S 
       34.06         6.02        29.16        13.64         4.24         3.62 
TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT 
        3.65         1.97         0.62         3.19         0.43        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       44.68        14.86         8.84         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

      18Q LOSS CNV 18Q LOSS WILD-TYPE 
              0.10               0.07 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             37.61              90.67 
      18Q LOSS CNV 18Q LOSS WILD-TYPE 
             7.580             13.955 
[1] "0.1 - 37.6 (7.6)"  "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 CNV" "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 CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        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-A3CH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "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 CNV" "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 CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        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-A3CH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "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 CNV" "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 CNV"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV"       "18Q LOSS CNV" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"18Q LOSS WILD-TYPE"       "18Q LOSS CNV" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"       "18Q LOSS CNV" 
        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-A3CH 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS CNV          4    6
  18Q LOSS WILD-TYPE   21   41
        clus
vv       18Q LOSS CNV 18Q LOSS WILD-TYPE
  FEMALE            4                 21
  MALE              6                 41
                    vv
clus                 M0 M1 MX
  18Q LOSS CNV        7  0  3
  18Q LOSS WILD-TYPE 41  1 20
D63V4, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  M0            7                 41
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  18Q LOSS CNV        5  0  5
  18Q LOSS WILD-TYPE 44  1 16
D63V5, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  N0            5                 44
  N1            0                  1
  NX            5                 16
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS CNV        8  1  0  1
  18Q LOSS WILD-TYPE 42  7  1  7
D63V6, multiclass
    clus
vv   18Q LOSS CNV 18Q LOSS WILD-TYPE
  R0            8                 42
  R1            1                  7
  R2            0                  1
  RX            1                  7
D63V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS CNV             5        1          2          0          0
  18Q LOSS WILD-TYPE      24       11         14          4          1
                    vv
clus                 STAGE IVB
  18Q LOSS CNV               0
  18Q LOSS WILD-TYPE         1
D63V8, multiclass

Clustering(64) Variable = 19p loss
D64V1, survival
                    sevent
clus2                 0  1
  19P LOSS CNV        4  1
  19P LOSS WILD-TYPE 36 25
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 5                 61 
      19P LOSS CNV 19P LOSS WILD-TYPE 
                 1                 25 
$`19P LOSS CNV`
TCGA-BC-A10W TCGA-DD-A11A TCGA-DD-A1EI TCGA-G3-A25S TCGA-G3-A3CH 
        2.99         2.60         6.02         1.22         6.31 

$`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-CC-A3MA TCGA-CC-A3MB TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        0.07         0.10         0.13        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29        22.78         7.33         0.46        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
       90.67        79.36        66.31        19.76        53.52         6.67 
TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA 
       34.06        29.16        13.64         4.24         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        1.97         0.62         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         0.13        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 

      19P LOSS CNV 19P LOSS WILD-TYPE 
              1.22               0.07 
      19P LOSS CNV 19P LOSS WILD-TYPE 
              6.31              90.67 
      19P LOSS CNV 19P LOSS WILD-TYPE 
              2.99              14.27 
[1] "1.2 - 6.3 (3.0)"   "0.1 - 90.7 (14.3)"
        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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        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-A3CH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        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-A3CH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
      "19P LOSS CNV" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        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-A3CH 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE"       "19P LOSS CNV" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS CNV          0    5
  19P LOSS WILD-TYPE   25   42
        clus
vv       19P LOSS CNV 19P LOSS WILD-TYPE
  FEMALE            0                 25
  MALE              5                 42
                    vv
clus                 M0 M1 MX
  19P LOSS CNV        4  0  1
  19P LOSS WILD-TYPE 44  1 22
D64V4, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  M0            4                 44
  M1            0                  1
  MX            1                 22
                    vv
clus                 N0 N1 NX
  19P LOSS CNV        4  0  1
  19P LOSS WILD-TYPE 45  1 20
D64V5, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  N0            4                 45
  N1            0                  1
  NX            1                 20
                    vv
clus                 R0 R1 R2 RX
  19P LOSS CNV        3  2  0  0
  19P LOSS WILD-TYPE 47  6  1  8
D64V6, multiclass
    clus
vv   19P LOSS CNV 19P LOSS WILD-TYPE
  R0            3                 47
  R1            2                  6
  R2            0                  1
  RX            0                  8
D64V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS CNV             3        0          1          0          0
  19P LOSS WILD-TYPE      26       12         15          4          1
                    vv
clus                 STAGE IVB
  19P LOSS CNV               0
  19P LOSS WILD-TYPE         1
D64V8, multiclass

Clustering(65) Variable = 21q loss
D65V1, survival
                    sevent
clus2                 0  1
  21Q LOSS CNV        4  3
  21Q LOSS WILD-TYPE 36 23
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 7                 59 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
                 3                 23 
$`21Q LOSS CNV`
TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-A3MB TCGA-DD-A11A TCGA-DD-A1EL TCGA-EP-A3RK 
       27.52         5.03         0.10         2.60        13.64         0.43 
TCGA-G3-A25S 
        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-CC-A3MA 
       13.81         0.26         8.28         0.07         4.24         0.07 
TCGA-CC-A3MC TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        0.13        55.17        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         0.46        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC 
       29.16         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 TCGA-G3-A25T 
        3.19        22.85        14.40        19.07         0.13        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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              0.10               0.07 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
             27.52              90.67 
      21Q LOSS CNV 21Q LOSS WILD-TYPE 
              2.60              14.27 
[1] "0.1 - 27.5 (2.6)"  "0.1 - 90.7 (14.3)"
        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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        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-A3CH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        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-A3CH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "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 CNV" "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 CNV" "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-CC-A3MA         TCGA-CC-A3MB 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-CC-A3MC         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 CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
      "21Q LOSS CNV" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE"       "21Q LOSS CNV" 
        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-A3CH 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "3.8"
D65V2, continuous
D65V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS CNV          0   10
  21Q LOSS WILD-TYPE   25   37
        clus
vv       21Q LOSS CNV 21Q LOSS WILD-TYPE
  FEMALE            0                 25
  MALE             10                 37
                    vv
clus                 M0 M1 MX
  21Q LOSS CNV        7  0  3
  21Q LOSS WILD-TYPE 41  1 20
D65V4, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  M0            7                 41
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  21Q LOSS CNV        7  0  3
  21Q LOSS WILD-TYPE 42  1 18
D65V5, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  N0            7                 42
  N1            0                  1
  NX            3                 18
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS CNV        4  2  0  1
  21Q LOSS WILD-TYPE 46  6  1  7
D65V6, multiclass
    clus
vv   21Q LOSS CNV 21Q LOSS WILD-TYPE
  R0            4                 46
  R1            2                  6
  R2            0                  1
  RX            1                  7
D65V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  21Q LOSS CNV             2        1          4          1          0
  21Q LOSS WILD-TYPE      27       11         12          3          1
                    vv
clus                 STAGE IVB
  21Q LOSS CNV               0
  21Q LOSS WILD-TYPE         1
D65V8, multiclass

Clustering(66) Variable = 22q loss
D66V1, survival
                    sevent
clus2                 0  1
  22Q LOSS CNV        5  2
  22Q LOSS WILD-TYPE 35 24
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 7                 59 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
                 2                 24 
$`22Q LOSS CNV`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-DD-A113 TCGA-EP-A2KB TCGA-G3-A25S 
       37.32        27.52        13.81        55.17         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-CC-A3MA TCGA-CC-A3MB 
        0.26         8.28         0.07         4.24         0.07         0.10 
TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        0.13        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-A1EA 
        2.60         0.46        21.44        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
       66.31        19.76        53.52         6.67        34.06         6.02 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC 
       29.16        13.64         4.24         3.62         3.65         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-FV-A3R3 
        3.19         0.43        22.85        14.40        19.07         0.13 
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-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

      22Q LOSS CNV 22Q LOSS WILD-TYPE 
              1.22               0.07 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             55.17              90.67 
      22Q LOSS CNV 22Q LOSS WILD-TYPE 
             27.52              11.57 
[1] "1.2 - 55.2 (27.5)" "0.1 - 90.7 (11.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "22Q LOSS CNV" "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-A3CH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "22Q LOSS CNV" "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-A3CH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "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 CNV" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        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 CNV" 
        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-CC-A3MA         TCGA-CC-A3MB 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-A3MC         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"       "22Q LOSS CNV" "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-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A12J         TCGA-EP-A26S         TCGA-EP-A2KA 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A2KB         TCGA-EP-A2KC         TCGA-EP-A3JL 
      "22Q LOSS CNV" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-FV-A3R3         TCGA-G3-A25S 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"       "22Q LOSS CNV" 
        TCGA-G3-A25T         TCGA-G3-A25U         TCGA-G3-A25V 
      "22Q LOSS CNV" "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-A3CH 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CI         TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D66V2, continuous
D66V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS CNV          6    3
  22Q LOSS WILD-TYPE   19   44
        clus
vv       22Q LOSS CNV 22Q LOSS WILD-TYPE
  FEMALE            6                 19
  MALE              3                 44
                    vv
clus                 M0 M1 MX
  22Q LOSS CNV        6  0  3
  22Q LOSS WILD-TYPE 42  1 20
D66V4, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  M0            6                 42
  M1            0                  1
  MX            3                 20
                    vv
clus                 N0 N1 NX
  22Q LOSS CNV        5  0  4
  22Q LOSS WILD-TYPE 44  1 17
D66V5, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  N0            5                 44
  N1            0                  1
  NX            4                 17
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS CNV        4  3  0  2
  22Q LOSS WILD-TYPE 46  5  1  6
D66V6, multiclass
    clus
vv   22Q LOSS CNV 22Q LOSS WILD-TYPE
  R0            4                 46
  R1            3                  5
  R2            0                  1
  RX            2                  6
D66V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  22Q LOSS CNV             2        3          1          1          0
  22Q LOSS WILD-TYPE      27        9         15          3          1
                    vv
clus                 STAGE IVB
  22Q LOSS CNV               0
  22Q LOSS WILD-TYPE         1
D66V8, multiclass
                       V1.D                          V2 
            "Time to Death"                       "AGE" 
                         V3                          V4 
                   "GENDER"        "DISTANT.METASTASIS" 
                         V5                          V6 
    "LYMPH.NODE.METASTASIS" "COMPLETENESS.OF.RESECTION" 
                         V7                          V8 
          "TUMOR.STAGECODE"     "NEOPLASM.DISEASESTAGE" 
> q(save="no")
