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

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

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

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

> source("/xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/tcga-gdac/Correlate_Clinical_Cnvsarms_onlysig/broadinstitute.org/cancer.genome.analysis/00498/19/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/00498/19/", "-nF=/xchip/tcga/Tools/Nozzle/v1.current", "-iD=/xchip/cga/gdac-prod/tcga-gdac/jobResults/cnvarms2cluster/LIHC-TP/2861074/broad_values_by_arm.mutsig.cluster.txt", "-iC=/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/LIHC-TP/2843149/1.GDAC_clinicalDataPicker.Finished/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=69, in cluster file=97, common to both=68
[1] "Reduce the number of clustering variables from 80 to 64."
[1] 64 68
[1] "1p gain mutation analysis"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                60 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                8                60 
[1] "1q gain mutation analysis"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               36                32 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               36                32 
[1] "2p gain mutation analysis"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                60 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                60 
[1] "2q gain mutation analysis"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                61 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                61 
[1] "3p gain mutation analysis"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                65 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                65 
[1] "3q gain mutation analysis"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                65 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                65 
[1] "4p gain mutation analysis"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                63 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                5                63 
[1] "5p gain mutation analysis"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20                48 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               20                48 
[1] "5q gain mutation analysis"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14                54 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               14                54 
[1] "6p gain mutation analysis"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                55 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                55 
[1] "6q gain mutation analysis"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9                59 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                9                59 
[1] "7p gain mutation analysis"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                50 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               18                50 
[1] "7q gain mutation analysis"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                49 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               19                49 
[1] "8p gain mutation analysis"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                57 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               11                57 
[1] "8q gain mutation analysis"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               33                35 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               33                35 
[1] "9p gain mutation analysis"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                65 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                3                65 
[1] "9q gain mutation analysis"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                65 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                3                65 
[1] "10p gain mutation analysis"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 63 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 5                 63 
[1] "12q gain mutation analysis"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 65 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 3                 65 
[1] "15q gain mutation analysis"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 63 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 63 
[1] "16p gain mutation analysis"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 65 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 65 
[1] "17p gain mutation analysis"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 65 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 65 
[1] "17q gain mutation analysis"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 51 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                17                 51 
[1] "18q gain mutation analysis"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 65 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 65 
[1] "19p gain mutation analysis"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 63 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 63 
[1] "19q gain mutation analysis"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 61 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 61 
[1] "20p gain mutation analysis"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 56 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                12                 56 
[1] "20q gain mutation analysis"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 55 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                13                 55 
[1] "21q gain mutation analysis"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 64 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 64 
[1] "22q gain mutation analysis"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 61 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 61 
[1] "Xq gain mutation analysis"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                64 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                64 
[1] "1p loss mutation analysis"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13                55 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               13                55 
[1] "1q loss mutation analysis"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                64 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                64 
[1] "2p loss mutation analysis"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                65 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                3                65 
[1] "2q loss mutation analysis"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                64 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4                64 
[1] "3p loss mutation analysis"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                63 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                63 
[1] "3q loss mutation analysis"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                65 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                65 
[1] "4p loss mutation analysis"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                59 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                9                59 
[1] "4q loss mutation analysis"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                52 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               16                52 
[1] "5q loss mutation analysis"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                64 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                64 
[1] "6q loss mutation analysis"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11                57 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               11                57 
[1] "7p loss mutation analysis"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                63 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                5                63 
[1] "7q loss mutation analysis"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                61 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                7                61 
[1] "8p loss mutation analysis"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               30                38 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               30                38 
[1] "8q loss mutation analysis"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                63 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                5                63 
[1] "9p loss mutation analysis"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               16                52 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               16                52 
[1] "9q loss mutation analysis"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                54 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                54 
[1] "10p loss mutation analysis"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 65 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 65 
[1] "10q loss mutation analysis"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 56 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                12                 56 
[1] "11p loss mutation analysis"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 63 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 63 
[1] "11q loss mutation analysis"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 60 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 8                 60 
[1] "12p loss mutation analysis"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 64 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 64 
[1] "13q loss mutation analysis"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                 45 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                23                 45 
[1] "14q loss mutation analysis"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                22                 46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                22                 46 
[1] "15q loss mutation analysis"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 61 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 7                 61 
[1] "16p loss mutation analysis"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                 54 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                14                 54 
[1] "16q loss mutation analysis"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                 46 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                22                 46 
[1] "17p loss mutation analysis"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 40 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                 40 
[1] "17q loss mutation analysis"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 65 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 65 
[1] "18p loss mutation analysis"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 61 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 61 
[1] "18q loss mutation analysis"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 59 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 59 
[1] "19p loss mutation analysis"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 63 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 63 
[1] "21q loss mutation analysis"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 59 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 9                 59 
[1] "22q loss mutation analysis"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 9                 59 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 9                 59 
[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 68 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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        1678           NA           NA           NA          693           NA 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
          79           NA          652           NA           NA         2414 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EI 
        2017          601         1628          203         1036          183 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
         887           NA          129          110          111           60 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
          NA           97           13           NA           NA           NA 
TCGA-FV-A3I1 TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
          NA           37         1175         1231          434          390 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
        1359           NA          269          253          192          179 
TCGA-G3-A3CJ TCGA-G3-A3CK 
         136           27 
Variable 1:'AGE':	nDistinctValues=36,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'DAYSTODEATH':	nDistinctValues=25,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 3:'DAYSTOLASTFOLLOWUP':	nDistinctValues=37,	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 
 31  13   9   8   2   5 
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 68 columns, 1 survival variables, and 7 non-survival variables.
AGE, nv=36, 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 mutation analysis
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED    4  3
  1P GAIN WILD-TYPE 32 23
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                7                55 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                23 
$`1P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-EP-A12J TCGA-EP-A26S 
       37.32        27.52         2.99        37.61         4.24         3.62 
TCGA-G3-A25W 
       12.82 

$`1P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X 
       48.99        11.57        10.13        46.78        27.52        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       23.34         1.12        69.57         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24        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-A2KA 
        6.67        34.06         6.02        29.16        13.64         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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
       19.07         1.22        38.63        40.47        14.27        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-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 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             2.99              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            37.61             90.67 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            12.82             14.27 
[1] "3.0 - 37.6 (12.8)" "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED"   "1P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE"   "1P GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P GAIN WILD-TYPE"   "1P GAIN MUTATED" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED      3    5
  1P GAIN WILD-TYPE   21   39
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               3                21
  MALE                 5                39
                   vv
clus                M0 M1 MX
  1P GAIN MUTATED    3  0  5
  1P GAIN WILD-TYPE 42  1 17
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               3                42
  M1               0                 1
  MX               5                17
                   vv
clus                N0 N1 NX
  1P GAIN MUTATED    3  0  5
  1P GAIN WILD-TYPE 43  1 15
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               3                43
  N1               0                 1
  NX               5                15
                   vv
clus                R0 R1 R2 RX
  1P GAIN MUTATED    3  3  0  0
  1P GAIN WILD-TYPE 43  5  1  8
D1V6, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0               3                43
  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 MUTATED         2        0          1          2          0         0
  1P GAIN WILD-TYPE      26       12         12          2          1         1
D1V8, multiclass

Clustering(2) Variable = 1q gain mutation analysis
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   20 12
  1Q GAIN WILD-TYPE 16 14
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32                30 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               12                14 
$`1Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A112 
       37.32        10.13        27.52         2.99        23.34         5.03 
TCGA-BC-A216 TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 
       37.61         8.28        55.17        37.74        22.78         7.33 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EH TCGA-DD-A1EL 
       21.44        90.67        79.36         6.67        34.06        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-FV-A2QR TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       19.07         1.22        12.82        44.68         8.84         8.32 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

$`1Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Z 
       48.99        11.57        46.78        27.52        25.32         1.12 
TCGA-BC-A110 TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A115 
       69.57        13.81         0.26         0.07         4.24        83.57 
TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EC 
       53.29         2.60         0.46        51.25        66.31        19.76 
TCGA-DD-A1ED TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
       53.52         6.02        29.16         0.43        22.85        14.40 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A3CI 
       38.63        40.47        14.27        14.86         6.31         5.88 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.62              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            90.67             83.57 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            9.485            17.310 
[1] "0.6 - 90.7 (9.5)"  "0.1 - 83.6 (17.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q GAIN WILD-TYPE"   "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" "1Q GAIN WILD-TYPE" "1Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "1Q GAIN MUTATED"   "1Q GAIN MUTATED" 
[1] "hr=" "1"  
D2V2, continuous
D2V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     10   26
  1Q GAIN WILD-TYPE   14   18
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              10                14
  MALE                26                18
                   vv
clus                M0 M1 MX
  1Q GAIN MUTATED   22  1 13
  1Q GAIN WILD-TYPE 23  0  9
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0              22                23
  M1               1                 0
  MX              13                 9
                   vv
clus                N0 N1 NX
  1Q GAIN MUTATED   23  0 12
  1Q GAIN WILD-TYPE 23  1  8
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              23                23
  N1               0                 1
  NX              12                 8
                   vv
clus                R0 R1 R2 RX
  1Q GAIN MUTATED   23  5  1  4
  1Q GAIN WILD-TYPE 23  3  0  4
D2V6, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              23                23
  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 MUTATED        13        9          4          3          0         1
  1Q GAIN WILD-TYPE      15        3          9          1          1         0
D2V8, multiclass

Clustering(3) Variable = 2p gain mutation analysis
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    3  5
  2P GAIN WILD-TYPE 33 21
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                54 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                5                21 
$`2P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-ES-A2HS TCGA-G3-A25T 
       48.99        37.32        10.13        27.52        22.85        38.63 
TCGA-G3-A25W TCGA-G3-A25Z 
       12.82         8.84 

$`2P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y 
       11.57        46.78        27.52         2.99        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        1.12        69.57         5.03        37.61        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24        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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
       14.40        19.07         1.22        40.47        14.27        44.68 
TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.32         6.31         5.88         4.47         0.89 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.84              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            48.99             90.67 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           25.185            13.725 
[1] "8.8 - 49.0 (25.2)" "0.1 - 90.7 (13.7)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2P GAIN MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "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 MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "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 MUTATED" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED"   "2P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2P GAIN WILD-TYPE"   "2P GAIN MUTATED" "2P GAIN WILD-TYPE" "2P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2P GAIN MUTATED" "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 MUTATED      5    3
  2P GAIN WILD-TYPE   19   41
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               5                19
  MALE                 3                41
                   vv
clus                M0 M1 MX
  2P GAIN MUTATED    4  0  4
  2P GAIN WILD-TYPE 41  1 18
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               4                41
  M1               0                 1
  MX               4                18
                   vv
clus                N0 N1 NX
  2P GAIN MUTATED    4  0  4
  2P GAIN WILD-TYPE 42  1 16
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0               4                42
  N1               0                 1
  NX               4                16
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED    5  3  0  0
  2P GAIN WILD-TYPE 41  5  1  8
D3V6, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0               5                41
  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 MUTATED         2        1          1          1          0         0
  2P GAIN WILD-TYPE      26       11         12          3          1         1
D3V8, multiclass

Clustering(4) Variable = 2q gain mutation analysis
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    3  4
  2Q GAIN WILD-TYPE 33 22
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                7                55 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                4                22 
$`2Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A25W 
       48.99        37.32        10.13        22.85        38.63        12.82 
TCGA-G3-A25Z 
        8.84 

$`2Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24        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-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-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.43        14.40        19.07         1.22        40.47        14.27 
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 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             8.84              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            48.99             90.67 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            22.85             13.81 
[1] "8.8 - 49.0 (22.9)" "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "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 MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "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 MUTATED" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED"   "2Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q GAIN WILD-TYPE"   "2Q GAIN MUTATED" "2Q GAIN WILD-TYPE" "2Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "2Q GAIN MUTATED" "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 MUTATED      5    2
  2Q GAIN WILD-TYPE   19   42
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               5                19
  MALE                 2                42
                   vv
clus                M0 M1 MX
  2Q GAIN MUTATED    4  0  3
  2Q GAIN WILD-TYPE 41  1 19
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               4                41
  M1               0                 1
  MX               3                19
                   vv
clus                N0 N1 NX
  2Q GAIN MUTATED    4  0  3
  2Q GAIN WILD-TYPE 42  1 17
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0               4                42
  N1               0                 1
  NX               3                17
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED    5  2  0  0
  2Q GAIN WILD-TYPE 41  6  1  8
D4V6, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0               5                41
  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 MUTATED         2        1          1          1          0         0
  2Q GAIN WILD-TYPE      26       11         12          3          1         1
D4V8, multiclass

Clustering(5) Variable = 3p gain mutation analysis
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED    2  1
  3P GAIN WILD-TYPE 34 25
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                3                59 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                1                25 
$`3P GAIN MUTATED`
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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24        55.17        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        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-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        3.19         0.43        14.40        19.07         1.22        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 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            21.44              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            29.16             90.67 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            22.85             13.64 
[1] "21.4 - 29.2 (22.9)" "0.1 - 90.7 (13.6)" 
       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-DD-A113 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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-DD-A113 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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-DD-A113 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P GAIN WILD-TYPE" "3P GAIN WILD-TYPE"   "3P GAIN MUTATED" "3P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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 MUTATED      1    2
  3P GAIN WILD-TYPE   23   42
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE               1                23
  MALE                 2                42
                   vv
clus                M0 M1 MX
  3P GAIN MUTATED    2  0  1
  3P GAIN WILD-TYPE 43  1 21
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  3P GAIN MUTATED    1  1  1
  3P GAIN WILD-TYPE 45  0 19
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0               1                45
  N1               1                 0
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  3P GAIN MUTATED    2  0  0  1
  3P GAIN WILD-TYPE 44  8  1  7
D5V6, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0               2                44
  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 MUTATED         2        0          0          0          1         0
  3P GAIN WILD-TYPE      26       12         13          4          0         1
D5V8, multiclass

Clustering(6) Variable = 3q gain mutation analysis
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED    2  1
  3Q GAIN WILD-TYPE 34 25
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                59 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                1                25 
$`3Q GAIN MUTATED`
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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24        55.17        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        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-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        3.19         0.43        14.40        19.07         1.22        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 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            21.44              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            29.16             90.67 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            22.85             13.64 
[1] "21.4 - 29.2 (22.9)" "0.1 - 90.7 (13.6)" 
       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-DD-A113 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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-DD-A113 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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-DD-A113 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q GAIN WILD-TYPE" "3Q GAIN WILD-TYPE"   "3Q GAIN MUTATED" "3Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        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 MUTATED      1    2
  3Q GAIN WILD-TYPE   23   42
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE               1                23
  MALE                 2                42
                   vv
clus                M0 M1 MX
  3Q GAIN MUTATED    2  0  1
  3Q GAIN WILD-TYPE 43  1 21
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  3Q GAIN MUTATED    1  1  1
  3Q GAIN WILD-TYPE 45  0 19
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0               1                45
  N1               1                 0
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED    2  0  0  1
  3Q GAIN WILD-TYPE 44  8  1  7
D6V6, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0               2                44
  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 MUTATED         2        0          0          0          1         0
  3Q GAIN WILD-TYPE      26       12         13          4          0         1
D6V8, multiclass

Clustering(7) Variable = 4p gain mutation analysis
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED    3  1
  4P GAIN WILD-TYPE 33 25
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                4                58 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                25 
$`4P GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EH 
       10.13        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-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-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-A1ED TCGA-DD-A1EE TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
       53.52         6.67         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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            10.13              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            34.06             90.67 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           21.270            13.725 
[1] "10.1 - 34.1 (21.3)" "0.1 - 90.7 (13.7)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "4P GAIN MUTATED" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE"   "4P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" "4P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED      3    2
  4P GAIN WILD-TYPE   21   42
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               3                21
  MALE                 2                42
                   vv
clus                M0 M1 MX
  4P GAIN MUTATED    4  0  1
  4P GAIN WILD-TYPE 41  1 21
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0               4                41
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  4P GAIN MUTATED    4  0  1
  4P GAIN WILD-TYPE 42  1 19
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               4                42
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  4P GAIN MUTATED    4  0  0  1
  4P GAIN WILD-TYPE 42  8  1  7
D7V6, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               4                42
  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 MUTATED         2        1          0          1          0         0
  4P GAIN WILD-TYPE      26       11         13          3          1         1
D7V8, multiclass

Clustering(8) Variable = 5p gain mutation analysis
D8V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED    9 10
  5P GAIN WILD-TYPE 27 16
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               19                43 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               10                16 
$`5P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A115 
       37.32         2.99         5.03         8.28         4.24        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
       53.29        22.78        51.25        90.67        79.36        66.31 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25W TCGA-G3-A25X 
        1.97         3.19        14.40        19.07        12.82        44.68 
TCGA-G3-A3CG 
        8.32 

$`5P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A11A 
        0.26         0.07        55.17        37.74         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
        0.46        21.44        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-A3RK TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.62         0.43        22.85         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.27        14.86         8.84         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             1.97              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            90.67             69.57 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            19.07             13.64 
[1] "2.0 - 90.7 (19.1)" "0.1 - 69.6 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "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 MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED"   "5P GAIN MUTATED" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE"   "5P GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "5P GAIN MUTATED" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED"   "5P GAIN MUTATED" "5P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5P GAIN WILD-TYPE"   "5P GAIN MUTATED" "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 MUTATED      7   13
  5P GAIN WILD-TYPE   17   31
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE               7                17
  MALE                13                31
                   vv
clus                M0 M1 MX
  5P GAIN MUTATED   14  0  6
  5P GAIN WILD-TYPE 31  1 16
D8V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0              14                31
  M1               0                 1
  MX               6                16
                   vv
clus                N0 N1 NX
  5P GAIN MUTATED   14  0  6
  5P GAIN WILD-TYPE 32  1 14
D8V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              14                32
  N1               0                 1
  NX               6                14
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   13  3  0  3
  5P GAIN WILD-TYPE 33  5  1  5
D8V6, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              13                33
  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 MUTATED         9        3          4          1          0         0
  5P GAIN WILD-TYPE      19        9          9          3          1         1
D8V8, multiclass

Clustering(9) Variable = 5q gain mutation analysis
D9V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED    5  8
  5Q GAIN WILD-TYPE 31 18
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               13                49 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                8                18 
$`5Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A112 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       37.32         2.99         5.03        83.57        53.29        22.78 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-EP-A2KB TCGA-ES-A2HT TCGA-G3-A25W 
       51.25        90.67        79.36         1.97        14.40        12.82 
TCGA-G3-A3CG 
        8.32 

$`5Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24        55.17        37.74 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EB TCGA-DD-A1EC 
        7.33         2.60         0.46        21.44        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-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       22.85        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             1.97              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            90.67             69.57 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            22.78             13.64 
[1] "2.0 - 90.7 (22.8)" "0.1 - 69.6 (13.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "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 MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "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 MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "5Q GAIN MUTATED"   "5Q GAIN MUTATED"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "5Q GAIN WILD-TYPE" "5Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"5Q GAIN WILD-TYPE"   "5Q GAIN MUTATED" "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 MUTATED      5    9
  5Q GAIN WILD-TYPE   19   35
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               5                19
  MALE                 9                35
                   vv
clus                M0 M1 MX
  5Q GAIN MUTATED    9  0  5
  5Q GAIN WILD-TYPE 36  1 17
D9V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               9                36
  M1               0                 1
  MX               5                17
                   vv
clus                N0 N1 NX
  5Q GAIN MUTATED    9  0  5
  5Q GAIN WILD-TYPE 37  1 15
D9V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                37
  N1               0                 1
  NX               5                15
                   vv
clus                R0 R1 R2 RX
  5Q GAIN MUTATED   10  3  0  1
  5Q GAIN WILD-TYPE 36  5  1  7
D9V6, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              10                36
  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 MUTATED         6        1          3          1          0         0
  5Q GAIN WILD-TYPE      22       11         10          3          1         1
D9V8, multiclass

Clustering(10) Variable = 6p gain mutation analysis
D10V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED    7  5
  6P GAIN WILD-TYPE 29 21
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               12                50 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                5                21 
$`6P GAIN MUTATED`
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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
       37.61        13.81         0.07        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       53.29        22.78         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-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-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U 
        3.19         0.43        14.40        19.07        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI 
       14.27        12.82        14.86         8.84         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.26              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            44.68             90.67 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            7.805            14.630 
[1] "0.3 - 44.7 (7.8)"  "0.1 - 90.7 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "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 MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "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 MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED"   "6P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6P GAIN WILD-TYPE" "6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "6P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6P GAIN WILD-TYPE"   "6P GAIN MUTATED" "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 MUTATED      3   10
  6P GAIN WILD-TYPE   21   34
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               3                21
  MALE                10                34
                   vv
clus                M0 M1 MX
  6P GAIN MUTATED    8  1  4
  6P GAIN WILD-TYPE 37  0 18
D10V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               8                37
  M1               1                 0
  MX               4                18
                   vv
clus                N0 N1 NX
  6P GAIN MUTATED    8  0  5
  6P GAIN WILD-TYPE 38  1 15
D10V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               8                38
  N1               0                 1
  NX               5                15
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED    7  3  1  2
  6P GAIN WILD-TYPE 39  5  0  6
D10V6, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0               7                39
  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 MUTATED         6        2          2          1          0         1
  6P GAIN WILD-TYPE      22       10         11          3          1         0
D10V8, multiclass

Clustering(11) Variable = 6q gain mutation analysis
D11V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED    5  3
  6Q GAIN WILD-TYPE 31 23
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8                54 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                23 
$`6Q GAIN MUTATED`
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-DD-A113 
        5.03        37.61        13.81         0.26         0.07        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A12J 
       53.52         6.67         6.02        29.16        13.64         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT 
        3.62         3.65         3.19         0.43        22.85        14.40 
TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       14.86         8.84         6.31         5.88         4.47         0.89 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.62              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            34.06             90.67 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            5.785            16.965 
[1] "0.6 - 34.1 (5.8)"  "0.1 - 90.7 (17.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "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-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "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-DD-A113 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED"   "6Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" "6Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"6Q GAIN WILD-TYPE"   "6Q GAIN MUTATED" "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 MUTATED      2    7
  6Q GAIN WILD-TYPE   22   37
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               2                22
  MALE                 7                37
                   vv
clus                M0 M1 MX
  6Q GAIN MUTATED    6  1  2
  6Q GAIN WILD-TYPE 39  0 20
D11V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               6                39
  M1               1                 0
  MX               2                20
                   vv
clus                N0 N1 NX
  6Q GAIN MUTATED    7  0  2
  6Q GAIN WILD-TYPE 39  1 18
D11V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               7                39
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED    4  2  1  2
  6Q GAIN WILD-TYPE 42  6  0  6
D11V6, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0               4                42
  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 MUTATED         4        1          2          1          0         1
  6Q GAIN WILD-TYPE      24       11         11          3          1         0
D11V8, multiclass

Clustering(12) Variable = 7p gain mutation analysis
D12V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED    9  6
  7P GAIN WILD-TYPE 27 20
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                47 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
                6                20 
$`7P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A 
       37.32        10.13        27.52        55.17        22.78         2.60 
TCGA-DD-A11D TCGA-DD-A1EC TCGA-DD-A1EE TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
       51.25        19.76         6.67         0.62         3.19        22.85 
TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
       38.63         8.32         4.47 

$`7P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 
        0.26         8.28         0.07         4.24        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.29         7.33         0.46        21.44        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-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT 
        4.24         3.62         3.65         1.97         0.43        14.40 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07         1.22        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       14.86         8.84         6.31         5.88         0.89 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.62              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            55.17             90.67 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            19.76             13.81 
[1] "0.6 - 55.2 (19.8)" "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED"   "7P GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7P GAIN WILD-TYPE"   "7P GAIN MUTATED" "7P GAIN WILD-TYPE" "7P GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7P GAIN MUTATED" "7P GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D12V2, continuous
D12V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      8   10
  7P GAIN WILD-TYPE   16   34
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE               8                16
  MALE                10                34
                   vv
clus                M0 M1 MX
  7P GAIN MUTATED   12  0  6
  7P GAIN WILD-TYPE 33  1 16
D12V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0              12                33
  M1               0                 1
  MX               6                16
                   vv
clus                N0 N1 NX
  7P GAIN MUTATED   12  0  6
  7P GAIN WILD-TYPE 34  1 14
D12V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              12                34
  N1               0                 1
  NX               6                14
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   11  3  0  2
  7P GAIN WILD-TYPE 35  5  1  6
D12V6, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              11                35
  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 MUTATED         8        3          3          1          0         0
  7P GAIN WILD-TYPE      20        9         10          3          1         1
D12V8, multiclass

Clustering(13) Variable = 7q gain mutation analysis
D13V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   10  6
  7Q GAIN WILD-TYPE 26 20
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               16                46 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
                6                20 
$`7Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10U TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11D 
       37.32        10.13        27.52        22.78         2.60        51.25 
TCGA-DD-A1EC TCGA-DD-A1EE TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL 
       19.76         6.67         3.62         3.65         0.62         3.19 
TCGA-ES-A2HS TCGA-G3-A25T TCGA-G3-A3CG TCGA-G3-A3CJ 
       22.85        38.63         8.32         4.47 

$`7Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W TCGA-BC-A10X 
       48.99        11.57        46.78        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24        55.17        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1E9 
       83.57        53.29         7.33         0.46        21.44        90.67 
TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       79.36        66.31        53.52        34.06         6.02        29.16 
TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A2KB TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR 
       13.64         4.24         1.97         0.43        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        40.47        14.27        12.82        44.68        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
        8.84         6.31         5.88         0.89 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.62              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            51.25             90.67 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            9.225            14.335 
[1] "0.6 - 51.2 (9.2)"  "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED"   "7Q GAIN MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "7Q GAIN MUTATED"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
"7Q GAIN WILD-TYPE"   "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" "7Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "7Q GAIN MUTATED" "7Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D13V2, continuous
D13V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      8   11
  7Q GAIN WILD-TYPE   16   33
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE               8                16
  MALE                11                33
                   vv
clus                M0 M1 MX
  7Q GAIN MUTATED   11  0  8
  7Q GAIN WILD-TYPE 34  1 14
D13V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0              11                34
  M1               0                 1
  MX               8                14
                   vv
clus                N0 N1 NX
  7Q GAIN MUTATED   12  0  7
  7Q GAIN WILD-TYPE 34  1 13
D13V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              12                34
  N1               0                 1
  NX               7                13
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   11  3  0  2
  7Q GAIN WILD-TYPE 35  5  1  6
D13V6, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              11                35
  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 MUTATED         9        2          4          1          0         0
  7Q GAIN WILD-TYPE      19       10          9          3          1         1
D13V8, multiclass

Clustering(14) Variable = 8p gain mutation analysis
D14V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED    7  3
  8P GAIN WILD-TYPE 29 23
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               10                52 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                3                23 
$`8P GAIN MUTATED`
TCGA-BC-A10S TCGA-CC-5258 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A1E9 TCGA-DD-A1EC 
       46.78         0.07         7.33         2.60        90.67        19.76 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-G3-A25X TCGA-G3-A25Z 
        1.97         3.19        44.68         8.84 

$`8P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A113 
       37.61        13.81         0.26         8.28         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11C 
       37.74        83.57        53.29        22.78         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EH 
       51.25        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-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-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A3CG 
       38.63        40.47        14.27        12.82        14.86         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.07              0.26 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            90.67             83.57 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            8.085            14.335 
[1] "0.1 - 90.7 (8.1)"  "0.3 - 83.6 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "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 MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "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 MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8P GAIN MUTATED"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8P GAIN MUTATED" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P GAIN WILD-TYPE" "8P GAIN WILD-TYPE"   "8P GAIN MUTATED" "8P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8P GAIN MUTATED" "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 MUTATED      2    9
  8P GAIN WILD-TYPE   22   35
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE               2                22
  MALE                 9                35
                   vv
clus                M0 M1 MX
  8P GAIN MUTATED    7  1  3
  8P GAIN WILD-TYPE 38  0 19
D14V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               7                38
  M1               1                 0
  MX               3                19
                   vv
clus                N0 N1 NX
  8P GAIN MUTATED    8  0  3
  8P GAIN WILD-TYPE 38  1 17
D14V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0               8                38
  N1               0                 1
  NX               3                17
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED    7  0  1  2
  8P GAIN WILD-TYPE 39  8  0  6
D14V6, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0               7                39
  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 MUTATED         6        2          1          0          0         1
  8P GAIN WILD-TYPE      22       10         12          4          1         0
D14V8, multiclass

Clustering(15) Variable = 8q gain mutation analysis
D15V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   20 10
  8Q GAIN WILD-TYPE 16 16
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               30                32 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               10                16 
$`8Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A3KF TCGA-CC-5258 
       48.99        46.78        27.52         2.99         0.26         0.07 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       55.17        53.29        22.78         7.33         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EC TCGA-DD-A1EE TCGA-DD-A1EI TCGA-EP-A12J TCGA-EP-A2KA 
       90.67        19.76         6.67         6.02         4.24         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-G3-A25T TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CJ 
       38.63        12.82        44.68         8.84         8.32         4.47 

$`8Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y 
       11.57        37.32        10.13        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        1.12        69.57         5.03        37.61        13.81         8.28 
TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
        4.24        37.74        83.57         0.46        51.25        79.36 
TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A26S 
       66.31        53.52        34.06        29.16        13.64         3.62 
TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25Y TCGA-G3-A3CH 
       19.07         1.22        40.47        14.27        14.86         6.31 
TCGA-G3-A3CI TCGA-G3-A3CK 
        5.88         0.89 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.07              0.46 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            90.67             83.57 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            8.580            16.965 
[1] "0.1 - 90.7 (8.6)"  "0.5 - 83.6 (17.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q GAIN WILD-TYPE"   "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "8Q GAIN MUTATED"   "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" "8Q GAIN WILD-TYPE" 
       TCGA-G3-A3CJ        TCGA-G3-A3CK 
  "8Q GAIN MUTATED" "8Q GAIN WILD-TYPE" 
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     10   23
  8Q GAIN WILD-TYPE   14   21
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              10                14
  MALE                23                21
                   vv
clus                M0 M1 MX
  8Q GAIN MUTATED   20  1 12
  8Q GAIN WILD-TYPE 25  0 10
D15V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0              20                25
  M1               1                 0
  MX              12                10
                   vv
clus                N0 N1 NX
  8Q GAIN MUTATED   21  0 12
  8Q GAIN WILD-TYPE 25  1  8
D15V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              21                25
  N1               0                 1
  NX              12                 8
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   22  4  1  3
  8Q GAIN WILD-TYPE 24  4  0  5
D15V6, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              22                24
  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 MUTATED        15        6          7          1          0         1
  8Q GAIN WILD-TYPE      13        6          6          3          1         0
D15V8, multiclass

Clustering(16) Variable = 9p gain mutation analysis
D16V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED    2  0
  9P GAIN WILD-TYPE 34 26
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                60 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                0                26 
$`9P GAIN MUTATED`
TCGA-EP-A2KB TCGA-G3-A25U 
        1.97        40.47 

$`9P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24        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-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         3.19         0.43        22.85        14.40        19.07 
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 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.97              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            40.47             90.67 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            21.22             14.04 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" "9P GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE"   "9P GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                60 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "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-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 MUTATED      2    1
  9P GAIN WILD-TYPE   22   43
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE               2                22
  MALE                 1                43
                   vv
clus                M0 M1 MX
  9P GAIN MUTATED    2  0  1
  9P GAIN WILD-TYPE 43  1 21
D16V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  9P GAIN MUTATED    2  0  1
  9P GAIN WILD-TYPE 44  1 19
D16V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED    2  0  0  1
  9P GAIN WILD-TYPE 44  8  1  7
D16V6, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0               2                44
  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 MUTATED         2        0          1          0          0         0
  9P GAIN WILD-TYPE      26       12         12          4          1         1
D16V8, multiclass

Clustering(17) Variable = 9q gain mutation analysis
D17V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED    2  0
  9Q GAIN WILD-TYPE 34 26
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                60 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                0                26 
$`9Q GAIN MUTATED`
TCGA-EP-A2KB TCGA-G3-A25U 
        1.97        40.47 

$`9Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        5.03        37.61        13.81         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24        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-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         3.19         0.43        22.85        14.40        19.07 
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 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.97              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            40.47             90.67 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            21.22             14.04 
[1] "2.0 - 40.5 (21.2)" "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE"   "9Q GAIN MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                60 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KC        TCGA-EP-A3JL 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "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-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 MUTATED      2    1
  9Q GAIN WILD-TYPE   22   43
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE               2                22
  MALE                 1                43
                   vv
clus                M0 M1 MX
  9Q GAIN MUTATED    2  0  1
  9Q GAIN WILD-TYPE 43  1 21
D17V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  9Q GAIN MUTATED    2  0  1
  9Q GAIN WILD-TYPE 44  1 19
D17V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED    2  0  0  1
  9Q GAIN WILD-TYPE 44  8  1  7
D17V6, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0               2                44
  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 MUTATED         2        0          1          0          0         0
  9Q GAIN WILD-TYPE      26       12         12          4          1         1
D17V8, multiclass

Clustering(18) Variable = 10p gain mutation analysis
D18V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    1  3
  10P GAIN WILD-TYPE 35 23
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 4                 58 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 3                 23 
$`10P GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-EP-A2KB TCGA-ES-A2HS 
       37.32        10.13         1.97        22.85 

$`10P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
       48.99        11.57        46.78        27.52        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
       25.32        23.34         1.12        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
        0.43        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.97               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             37.32              90.67 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             16.49              14.04 
[1] "2.0 - 37.3 (16.5)" "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE"   "10P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10P GAIN MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"10P GAIN WILD-TYPE"   "10P GAIN MUTATED" "10P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
[1] "hr=" "2.9"
D18V2, continuous
D18V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      3    2
  10P GAIN WILD-TYPE   21   42
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  10P GAIN MUTATED    1  0  4
  10P GAIN WILD-TYPE 44  1 18
D18V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                1                 44
  M1                0                  1
  MX                4                 18
                    vv
clus                 N0 N1 NX
  10P GAIN MUTATED    1  0  4
  10P GAIN WILD-TYPE 45  1 16
D18V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                1                 45
  N1                0                  1
  NX                4                 16
                    vv
clus                 R0 R1 R2 RX
  10P GAIN MUTATED    3  1  0  1
  10P GAIN WILD-TYPE 43  7  1  7
D18V6, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0                3                 43
  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 MUTATED         2        0          1          0          0
  10P GAIN WILD-TYPE      26       12         12          4          1
                    vv
clus                 STAGE IVB
  10P GAIN MUTATED           0
  10P GAIN WILD-TYPE         1
D18V8, multiclass

Clustering(19) Variable = 12q gain mutation analysis
D19V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED    2  0
  12Q GAIN WILD-TYPE 34 26
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 60 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 0                 26 
$`12Q GAIN MUTATED`
TCGA-BC-A3KF TCGA-G3-A25T 
        0.26        38.63 

$`12Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61        13.81         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       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-A2HS TCGA-ES-A2HT TCGA-FV-A2QR 
        0.62         3.19         0.43        22.85        14.40        19.07 
TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y 
        1.22        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 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.26               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             38.63              90.67 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            19.445             14.040 
[1] "0.3 - 38.6 (19.4)" "0.1 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "12Q GAIN MUTATED" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE"   "12Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
[1] "Remove cluster labels:" "12Q GAIN MUTATED"      
clus
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 2                 60 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-BC-A3KG         TCGA-CC-5258         TCGA-CC-5263 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A113         TCGA-DD-A114         TCGA-DD-A115 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A116         TCGA-DD-A118         TCGA-DD-A119 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11A         TCGA-DD-A11B         TCGA-DD-A11C 
"12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" "12Q GAIN WILD-TYPE" 
        TCGA-DD-A11D         TCGA-DD-A1E9         TCGA-DD-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-G3-A25S         TCGA-G3-A25U         TCGA-G3-A25V 
"12Q GAIN WILD-TYPE" "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" 
D19V2, continuous
D19V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      2    1
  12Q GAIN WILD-TYPE   22   43
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                  1                 43
                    vv
clus                 M0 M1 MX
  12Q GAIN MUTATED    3  0  0
  12Q GAIN WILD-TYPE 42  1 22
D19V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                3                 42
  M1                0                  1
  MX                0                 22
                    vv
clus                 N0 N1 NX
  12Q GAIN MUTATED    2  0  1
  12Q GAIN WILD-TYPE 44  1 19
D19V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                1                 19
                    vv
clus                 R0 R1 R2 RX
  12Q GAIN MUTATED    2  0  0  1
  12Q GAIN WILD-TYPE 44  8  1  7
D19V6, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0                2                 44
  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 MUTATED         1        1          1          0          0
  12Q GAIN WILD-TYPE      27       11         12          4          1
                    vv
clus                 STAGE IVB
  12Q GAIN MUTATED           0
  12Q GAIN WILD-TYPE         1
D19V8, multiclass

Clustering(20) Variable = 15q gain mutation analysis
D20V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED    2  3
  15Q GAIN WILD-TYPE 34 23
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 5                 57 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                 23 
$`15Q GAIN MUTATED`
TCGA-BC-A10Q TCGA-BC-A10Y TCGA-BC-A3KG TCGA-ES-A2HS TCGA-G3-A25T 
       37.32        23.34         8.28        22.85        38.63 

$`15Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32         1.12        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
       13.81         0.26         0.07         4.24        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-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-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
        0.43        14.40        19.07         1.22        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 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.28               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             38.63              90.67 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             23.34              13.64 
[1] "8.3 - 38.6 (23.3)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "15Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE"   "15Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D20V2, continuous
D20V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    2
  15Q GAIN WILD-TYPE   21   42
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  15Q GAIN MUTATED    2  0  3
  15Q GAIN WILD-TYPE 43  1 19
D20V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                2                 43
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  15Q GAIN MUTATED    2  0  3
  15Q GAIN WILD-TYPE 44  1 17
D20V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  15Q GAIN MUTATED    4  1  0  0
  15Q GAIN WILD-TYPE 42  7  1  8
D20V6, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                4                 42
  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 MUTATED         1        2          0          0          0
  15Q GAIN WILD-TYPE      27       10         13          4          1
                    vv
clus                 STAGE IVB
  15Q GAIN MUTATED           0
  15Q GAIN WILD-TYPE         1
D20V8, multiclass

Clustering(21) Variable = 16p gain mutation analysis
D21V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED    1  2
  16P GAIN WILD-TYPE 35 24
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 3                 59 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 2                 24 
$`16P GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A11A 
       10.13         5.03         2.60 

$`16P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        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 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              2.60               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             10.13              90.67 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              5.03              14.40 
[1] "2.6 - 10.1 (5.0)"  "0.1 - 90.7 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-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-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" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-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-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" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "16P GAIN MUTATED" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P GAIN WILD-TYPE"   "16P GAIN MUTATED" "16P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-DD-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-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" 
[1] "hr=" "7.8"
D21V2, continuous
D21V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      1    2
  16P GAIN WILD-TYPE   23   42
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  16P GAIN MUTATED    1  0  2
  16P GAIN WILD-TYPE 44  1 20
D21V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                1                 44
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  16P GAIN MUTATED    1  0  2
  16P GAIN WILD-TYPE 45  1 18
D21V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0                1                 45
  N1                0                  1
  NX                2                 18
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED    3  0  0  0
  16P GAIN WILD-TYPE 43  8  1  8
D21V6, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0                3                 43
  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 MUTATED         1        0          0          0          0
  16P GAIN WILD-TYPE      27       12         13          4          1
                    vv
clus                 STAGE IVB
  16P GAIN MUTATED           0
  16P GAIN WILD-TYPE         1
D21V8, multiclass
[1] "Remove cluster labels:" "16P GAIN MUTATED"      
clus
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 1                 58 
        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-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-G3-A25S         TCGA-G3-A25T         TCGA-G3-A25U 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25V         TCGA-G3-A25W         TCGA-G3-A25X 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A25Y         TCGA-G3-A25Z         TCGA-G3-A3CG 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CH         TCGA-G3-A3CI         TCGA-G3-A3CJ 
"16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" "16P GAIN WILD-TYPE" 
        TCGA-G3-A3CK 
"16P GAIN WILD-TYPE" 

Clustering(22) Variable = 17p gain mutation analysis
D22V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED    1  2
  17P GAIN WILD-TYPE 35 24
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 3                 59 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 24 
$`17P GAIN MUTATED`
TCGA-BC-A10Q TCGA-EP-A2KB TCGA-ES-A2HS 
       37.32         1.97        22.85 

$`17P GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       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-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-G3-A25S TCGA-G3-A25T 
        3.19         0.43        14.40        19.07         1.22        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 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              1.97               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             37.32              90.67 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             22.85              13.81 
[1] "2.0 - 37.3 (22.9)" "0.1 - 90.7 (13.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE"   "17P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17P GAIN WILD-TYPE"   "17P GAIN MUTATED" "17P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P GAIN WILD-TYPE" "17P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D22V2, continuous
D22V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      2    1
  17P GAIN WILD-TYPE   22   43
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                2                 22
  MALE                  1                 43
                    vv
clus                 M0 M1 MX
  17P GAIN MUTATED    0  0  3
  17P GAIN WILD-TYPE 45  1 19
D22V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                0                 45
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  17P GAIN MUTATED    0  0  3
  17P GAIN WILD-TYPE 46  1 17
D22V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                0                 46
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  17P GAIN MUTATED    2  1  0  0
  17P GAIN WILD-TYPE 44  7  1  8
D22V6, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                2                 44
  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 MUTATED         2        0          0          0          0
  17P GAIN WILD-TYPE      26       12         13          4          1
                    vv
clus                 STAGE IVB
  17P GAIN MUTATED           0
  17P GAIN WILD-TYPE         1
D22V8, multiclass
[1] "Remove cluster labels:" "17P GAIN MUTATED"      
clus
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 2                 57 
        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-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-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" 

Clustering(23) Variable = 17q gain mutation analysis
D23V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED    7  9
  17Q GAIN WILD-TYPE 29 17
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                16                 46 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 9                 17 
$`17Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       48.99        37.32         2.99        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-CC-5263 TCGA-DD-A114 TCGA-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-DD-A113 
       69.57        37.61         0.26         8.28         0.07        55.17 
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-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.44        51.25        90.67        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-G3-A25S TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y 
       19.07         1.22        38.63        14.27        44.68        14.86 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
        8.32         6.31         5.88         4.47 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.89               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             79.36              90.67 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            13.315             14.335 
[1] "0.9 - 79.4 (13.3)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "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 MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "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 MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
  "17Q GAIN MUTATED"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
  "17Q GAIN MUTATED" "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 MUTATED" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "17Q GAIN MUTATED" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" "17Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q GAIN WILD-TYPE"   "17Q GAIN MUTATED" 
[1] "hr=" "1.9"
D23V2, continuous
D23V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      7   10
  17Q GAIN WILD-TYPE   17   34
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE                7                 17
  MALE                 10                 34
                    vv
clus                 M0 M1 MX
  17Q GAIN MUTATED   10  0  7
  17Q GAIN WILD-TYPE 35  1 15
D23V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0               10                 35
  M1                0                  1
  MX                7                 15
                    vv
clus                 N0 N1 NX
  17Q GAIN MUTATED    9  0  7
  17Q GAIN WILD-TYPE 37  1 13
D23V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0                9                 37
  N1                0                  1
  NX                7                 13
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED   12  3  0  2
  17Q GAIN WILD-TYPE 34  5  1  6
D23V6, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               12                 34
  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 MUTATED         6        4          2          1          0
  17Q GAIN WILD-TYPE      22        8         11          3          1
                    vv
clus                 STAGE IVB
  17Q GAIN MUTATED           0
  17Q GAIN WILD-TYPE         1
D23V8, multiclass

Clustering(24) Variable = 18q gain mutation analysis
D24V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED    2  1
  18Q GAIN WILD-TYPE 34 25
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 3                 59 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 1                 25 
$`18Q GAIN MUTATED`
TCGA-CC-5263 TCGA-DD-A113 TCGA-G3-A25X 
        4.24        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-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-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-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-G3-A25S 
        3.19         0.43        22.85        14.40        19.07         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z 
       38.63        40.47        14.27        12.82        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              4.24               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             55.17              90.67 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             44.68              13.81 
[1] "4.2 - 55.2 (44.7)" "0.1 - 90.7 (13.8)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "18Q GAIN MUTATED"   "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "18Q GAIN MUTATED" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q GAIN WILD-TYPE" "18Q GAIN WILD-TYPE" 
[1] "hr=" "1.9"
D24V2, continuous
D24V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    2
  18Q GAIN WILD-TYPE   23   42
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 23
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  18Q GAIN MUTATED    3  0  0
  18Q GAIN WILD-TYPE 42  1 22
D24V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                3                 42
  M1                0                  1
  MX                0                 22
                    vv
clus                 N0 N1 NX
  18Q GAIN MUTATED    3  0  0
  18Q GAIN WILD-TYPE 43  1 20
D24V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                3                 43
  N1                0                  1
  NX                0                 20
                    vv
clus                 R0 R1 R2 RX
  18Q GAIN MUTATED    2  0  0  1
  18Q GAIN WILD-TYPE 44  8  1  7
D24V6, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                2                 44
  R1                0                  8
  R2                0                  1
  RX                1                  7
D24V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18Q GAIN MUTATED         0        2          1          0          0
  18Q GAIN WILD-TYPE      28       10         12          4          1
                    vv
clus                 STAGE IVB
  18Q GAIN MUTATED           0
  18Q GAIN WILD-TYPE         1
D24V8, multiclass

Clustering(25) Variable = 19p gain mutation analysis
D25V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED    4  1
  19P GAIN WILD-TYPE 32 25
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 5                 57 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 1                 25 
$`19P GAIN MUTATED`
TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       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-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A 
        4.24        37.74        83.57        53.29         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        0.46        21.44        51.25        90.67        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-A3JL TCGA-EP-A3RK 
        4.24         3.62         3.65         0.62         3.19         0.43 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-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 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              1.97               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             55.17              90.67 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             22.78              13.64 
[1] "2.0 - 55.2 (22.8)" "0.1 - 90.7 (13.6)"
        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-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        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 MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        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 MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE"   "19P GAIN MUTATED" 
        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 MUTATED" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19P GAIN WILD-TYPE"   "19P GAIN MUTATED" "19P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P GAIN WILD-TYPE" "19P GAIN WILD-TYPE" 
[1] "hr=" "2.2"
D25V2, continuous
D25V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      4    1
  19P GAIN WILD-TYPE   20   43
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE                4                 20
  MALE                  1                 43
                    vv
clus                 M0 M1 MX
  19P GAIN MUTATED    3  0  2
  19P GAIN WILD-TYPE 42  1 20
D25V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                3                 42
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  19P GAIN MUTATED    3  0  2
  19P GAIN WILD-TYPE 43  1 18
D25V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0                3                 43
  N1                0                  1
  NX                2                 18
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED    5  0  0  0
  19P GAIN WILD-TYPE 41  8  1  8
D25V6, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0                5                 41
  R1                0                  8
  R2                0                  1
  RX                0                  8
D25V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19P GAIN MUTATED         4        1          0          0          0
  19P GAIN WILD-TYPE      24       11         13          4          1
                    vv
clus                 STAGE IVB
  19P GAIN MUTATED           0
  19P GAIN WILD-TYPE         1
D25V8, multiclass

Clustering(26) Variable = 19q gain mutation analysis
D26V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED    5  2
  19Q GAIN WILD-TYPE 31 24
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 7                 55 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 24 
$`19Q GAIN MUTATED`
TCGA-BC-A10R TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A1EC TCGA-EP-A2KB TCGA-ES-A2HS 
       10.13        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-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-A1ED 
       21.44        51.25        90.67        79.36        66.31        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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       19.07         1.22        38.63        40.47        14.27        12.82 
TCGA-G3-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 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              1.97               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             55.17              90.67 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             22.78              13.64 
[1] "2.0 - 55.2 (22.8)" "0.1 - 90.7 (13.6)"
        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 MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        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 MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        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 MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" 
        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 MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"19Q GAIN WILD-TYPE"   "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "19Q GAIN MUTATED" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19Q GAIN WILD-TYPE" "19Q GAIN WILD-TYPE" 
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      5    2
  19Q GAIN WILD-TYPE   19   42
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE                5                 19
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  19Q GAIN MUTATED    4  0  3
  19Q GAIN WILD-TYPE 41  1 19
D26V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                4                 41
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  19Q GAIN MUTATED    4  0  3
  19Q GAIN WILD-TYPE 42  1 17
D26V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0                4                 42
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  19Q GAIN MUTATED    7  0  0  0
  19Q GAIN WILD-TYPE 39  8  1  8
D26V6, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0                7                 39
  R1                0                  8
  R2                0                  1
  RX                0                  8
D26V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19Q GAIN MUTATED         4        2          0          0          0
  19Q GAIN WILD-TYPE      24       10         13          4          1
                    vv
clus                 STAGE IVB
  19Q GAIN MUTATED           0
  19Q GAIN WILD-TYPE         1
D26V8, multiclass

Clustering(27) Variable = 20p gain mutation analysis
D27V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED    5  5
  20P GAIN WILD-TYPE 31 21
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                10                 52 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                 5                 21 
$`20P GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-DD-A118 TCGA-DD-A11B 
       48.99        37.32        10.13         0.26        22.78         0.46 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
        1.97         3.19        22.85         1.22 

$`20P GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
       53.29         7.33         2.60        21.44        51.25        90.67 
TCGA-DD-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-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U 
        0.62         0.43        14.40        19.07        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 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.26               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             48.99              90.67 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             6.660             14.335 
[1] "0.3 - 49.0 (6.7)"  "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20P GAIN MUTATED" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20P GAIN WILD-TYPE"   "20P GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20P GAIN WILD-TYPE"   "20P GAIN MUTATED" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20P GAIN WILD-TYPE" "20P GAIN WILD-TYPE" 
[1] "hr=" "2.4"
D27V2, continuous
D27V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      6    6
  20P GAIN WILD-TYPE   18   38
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE                6                 18
  MALE                  6                 38
                    vv
clus                 M0 M1 MX
  20P GAIN MUTATED    7  0  5
  20P GAIN WILD-TYPE 38  1 17
D27V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                7                 38
  M1                0                  1
  MX                5                 17
                    vv
clus                 N0 N1 NX
  20P GAIN MUTATED    6  0  6
  20P GAIN WILD-TYPE 40  1 14
D27V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0                6                 40
  N1                0                  1
  NX                6                 14
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED    5  3  0  3
  20P GAIN WILD-TYPE 41  5  1  5
D27V6, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0                5                 41
  R1                3                  5
  R2                0                  1
  RX                3                  5
D27V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  20P GAIN MUTATED         7        1          2          0          0
  20P GAIN WILD-TYPE      21       11         11          4          1
                    vv
clus                 STAGE IVB
  20P GAIN MUTATED           0
  20P GAIN WILD-TYPE         1
D27V8, multiclass

Clustering(28) Variable = 20q gain mutation analysis
D28V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED    6  5
  20Q GAIN WILD-TYPE 30 21
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                11                 51 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                 5                 21 
$`20Q GAIN MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A3KF TCGA-DD-A118 TCGA-DD-A11B 
       48.99        37.32        10.13         0.26        22.78         0.46 
TCGA-DD-A11C TCGA-EP-A2KB TCGA-EP-A3JL TCGA-ES-A2HS TCGA-G3-A25S 
       21.44         1.97         3.19        22.85         1.22 

$`20Q GAIN WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X 
       11.57        46.78        27.52        27.52         2.99        25.32 
TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 
       23.34         1.12        69.57         5.03        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.29         7.33         2.60        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-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.43        14.40        19.07        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-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 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.26               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             48.99              90.67 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             10.13              14.27 
[1] "0.3 - 49.0 (10.1)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"20Q GAIN WILD-TYPE"   "20Q GAIN MUTATED" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"20Q GAIN WILD-TYPE" "20Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D28V2, continuous
D28V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      6    7
  20Q GAIN WILD-TYPE   18   37
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE                6                 18
  MALE                  7                 37
                    vv
clus                 M0 M1 MX
  20Q GAIN MUTATED    8  0  5
  20Q GAIN WILD-TYPE 37  1 17
D28V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0                8                 37
  M1                0                  1
  MX                5                 17
                    vv
clus                 N0 N1 NX
  20Q GAIN MUTATED    7  0  6
  20Q GAIN WILD-TYPE 39  1 14
D28V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0                7                 39
  N1                0                  1
  NX                6                 14
                    vv
clus                 R0 R1 R2 RX
  20Q GAIN MUTATED    5  3  0  4
  20Q GAIN WILD-TYPE 41  5  1  4
D28V6, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0                5                 41
  R1                3                  5
  R2                0                  1
  RX                4                  4
D28V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  20Q GAIN MUTATED         8        1          2          0          0
  20Q GAIN WILD-TYPE      20       11         11          4          1
                    vv
clus                 STAGE IVB
  20Q GAIN MUTATED           0
  20Q GAIN WILD-TYPE         1
D28V8, multiclass

Clustering(29) Variable = 21q gain mutation analysis
D29V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED    3  1
  21Q GAIN WILD-TYPE 33 25
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 4                 58 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 1                 25 
$`21Q GAIN MUTATED`
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-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
        4.24        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25U 
        3.19         0.43        14.40        19.07         1.22        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              1.97               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             55.17              90.67 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            30.740             13.725 
[1] "2.0 - 55.2 (30.7)" "0.1 - 90.7 (13.7)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" "21Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE"   "21Q GAIN MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q GAIN WILD-TYPE" "21Q GAIN WILD-TYPE" 
[1] "hr=" "2.3"
D29V2, continuous
D29V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      3    1
  21Q GAIN WILD-TYPE   21   43
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                3                 21
  MALE                  1                 43
                    vv
clus                 M0 M1 MX
  21Q GAIN MUTATED    2  0  2
  21Q GAIN WILD-TYPE 43  1 20
D29V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                2                 43
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  21Q GAIN MUTATED    2  0  2
  21Q GAIN WILD-TYPE 44  1 18
D29V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                2                 18
                    vv
clus                 R0 R1 R2 RX
  21Q GAIN MUTATED    4  0  0  0
  21Q GAIN WILD-TYPE 42  8  1  8
D29V6, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                4                 42
  R1                0                  8
  R2                0                  1
  RX                0                  8
D29V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  21Q GAIN MUTATED         2        2          0          0          0
  21Q GAIN WILD-TYPE      26       10         13          4          1
                    vv
clus                 STAGE IVB
  21Q GAIN MUTATED           0
  21Q GAIN WILD-TYPE         1
D29V8, multiclass

Clustering(30) Variable = 22q gain mutation analysis
D30V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED    2  5
  22Q GAIN WILD-TYPE 34 21
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 7                 55 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 5                 21 
$`22Q GAIN MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-DD-A118 TCGA-DD-A11D TCGA-DD-A1EJ TCGA-ES-A2HS 
       10.13         5.03        22.78        51.25        29.16        22.85 
TCGA-FV-A2QR 
       19.07 

$`22Q GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        83.57        53.29         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED 
       21.44        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-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 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              5.03               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             51.25              90.67 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             22.78              13.64 
[1] "5.0 - 51.2 (22.8)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q GAIN WILD-TYPE"   "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "22Q GAIN WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
  "22Q GAIN MUTATED" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q GAIN WILD-TYPE" "22Q GAIN WILD-TYPE" 
[1] "hr=" "2.1"
D30V2, continuous
D30V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    3
  22Q GAIN WILD-TYPE   20   41
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                 20
  MALE                  3                 41
                    vv
clus                 M0 M1 MX
  22Q GAIN MUTATED    4  0  3
  22Q GAIN WILD-TYPE 41  1 19
D30V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                4                 41
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  22Q GAIN MUTATED    3  1  3
  22Q GAIN WILD-TYPE 43  0 17
D30V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                3                 43
  N1                1                  0
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  22Q GAIN MUTATED    6  0  0  1
  22Q GAIN WILD-TYPE 40  8  1  7
D30V6, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                6                 40
  R1                0                  8
  R2                0                  1
  RX                1                  7
D30V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  22Q GAIN MUTATED         4        0          0          0          1
  22Q GAIN WILD-TYPE      24       12         13          4          0
                    vv
clus                 STAGE IVB
  22Q GAIN MUTATED           0
  22Q GAIN WILD-TYPE         1
D30V8, multiclass

Clustering(31) Variable = Xq gain mutation analysis
D31V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED    2  2
  XQ GAIN WILD-TYPE 34 24
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                4                58 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                2                24 
$`XQ GAIN MUTATED`
TCGA-BC-A10U TCGA-BC-A10Z TCGA-DD-A11A TCGA-EP-A12J 
       27.52         1.12         2.60         4.24 

$`XQ GAIN WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
        2.99        25.32        23.34        69.57         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U 
       22.85        14.40        19.07         1.22        38.63        40.47 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             1.12              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            27.52             90.67 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            3.420            14.335 
[1] "1.1 - 27.5 (3.4)"  "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE"   "XQ GAIN MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" "XQ GAIN WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D31V2, continuous
D31V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      1    3
  XQ GAIN WILD-TYPE   23   41
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE               1                23
  MALE                 3                41
                   vv
clus                M0 M1 MX
  XQ GAIN MUTATED    1  0  3
  XQ GAIN WILD-TYPE 44  1 19
D31V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               1                44
  M1               0                 1
  MX               3                19
                   vv
clus                N0 N1 NX
  XQ GAIN MUTATED    2  0  2
  XQ GAIN WILD-TYPE 44  1 18
D31V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED    3  1  0  0
  XQ GAIN WILD-TYPE 43  7  1  8
D31V6, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0               3                43
  R1               1                 7
  R2               0                 1
  RX               0                 8
D31V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  XQ GAIN MUTATED         3        0          0          0          0         0
  XQ GAIN WILD-TYPE      25       12         13          4          1         1
D31V8, multiclass

Clustering(32) Variable = 1p loss mutation analysis
D32V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED    7  5
  1P LOSS WILD-TYPE 29 21
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               12                50 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                21 
$`1P LOSS MUTATED`
TCGA-BC-A10S TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EH 
       46.78        55.17        22.78         0.46        51.25        34.06 
TCGA-DD-A1EJ TCGA-EP-A2KB TCGA-EP-A2KC TCGA-ES-A2HS TCGA-G3-A25S TCGA-G3-A25U 
       29.16         1.97         0.62        22.85         1.22        40.47 

$`1P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C 
       37.74        83.57        53.29         7.33         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-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-A1EI TCGA-DD-A1EL TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A3JL 
        6.02        13.64         4.24         3.62         3.65         3.19 
TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
        0.43        14.40        19.07        38.63        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 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.46              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            55.17             90.67 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           26.005            13.230 
[1] "0.5 - 55.2 (26.0)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
  "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED"   "1P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1P LOSS WILD-TYPE"   "1P LOSS MUTATED" "1P LOSS WILD-TYPE"   "1P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" "1P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D32V2, continuous
D32V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      6    7
  1P LOSS WILD-TYPE   18   37
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE               6                18
  MALE                 7                37
                   vv
clus                M0 M1 MX
  1P LOSS MUTATED    9  0  4
  1P LOSS WILD-TYPE 36  1 18
D32V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               9                36
  M1               0                 1
  MX               4                18
                   vv
clus                N0 N1 NX
  1P LOSS MUTATED    8  1  4
  1P LOSS WILD-TYPE 38  0 16
D32V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0               8                38
  N1               1                 0
  NX               4                16
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   10  1  0  2
  1P LOSS WILD-TYPE 36  7  1  6
D32V6, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              10                36
  R1               1                 7
  R2               0                 1
  RX               2                 6
D32V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1P LOSS MUTATED         8        2          0          1          1         0
  1P LOSS WILD-TYPE      20       10         13          3          0         1
D32V8, multiclass

Clustering(33) Variable = 1q loss mutation analysis
D33V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED    2  2
  1Q LOSS WILD-TYPE 34 24
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                58 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                2                24 
$`1Q LOSS MUTATED`
TCGA-BC-A10S TCGA-DD-A1EJ TCGA-ES-A2HS TCGA-G3-A25U 
       46.78        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-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-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        3.19         0.43        14.40        19.07         1.22        38.63 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       14.27        12.82        44.68        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            22.85              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            46.78             90.67 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           34.815            13.230 
[1] "22.9 - 46.8 (34.8)" "0.1 - 90.7 (13.2)" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
  "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" "1Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE"   "1Q LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" "1Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D33V2, continuous
D33V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2    2
  1Q LOSS WILD-TYPE   22   42
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               2                22
  MALE                 2                42
                   vv
clus                M0 M1 MX
  1Q LOSS MUTATED    2  0  2
  1Q LOSS WILD-TYPE 43  1 20
D33V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               2                20
                   vv
clus                N0 N1 NX
  1Q LOSS MUTATED    1  1  2
  1Q LOSS WILD-TYPE 45  0 18
D33V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0               1                45
  N1               1                 0
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  1Q LOSS MUTATED    4  0  0  0
  1Q LOSS WILD-TYPE 42  8  1  8
D33V6, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0               4                42
  R1               0                 8
  R2               0                 1
  RX               0                 8
D33V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  1Q LOSS MUTATED         2        0          0          0          1         0
  1Q LOSS WILD-TYPE      26       12         13          4          0         1
D33V8, multiclass

Clustering(34) Variable = 2p loss mutation analysis
D34V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED    2  0
  2P LOSS WILD-TYPE 34 26
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                60 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                0                26 
$`2P LOSS MUTATED`
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-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-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.25        90.67        79.36        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-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-G3-A25S 
        3.19         0.43        22.85        14.40        19.07         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 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.26              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            21.44             90.67 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            10.85             14.04 
[1] "0.3 - 21.4 (10.9)" "0.1 - 90.7 (14.0)"
       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 MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        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 MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        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 MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE"   "2P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        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 MUTATED"       
clus
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                2                60 
       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-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-A2QR        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" 
D34V2, continuous
[1] "Remove cluster labels:" "2P LOSS MUTATED"       
clus
  2P LOSS MUTATED 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-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-DD-A113 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11D 
"2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "2P LOSS WILD-TYPE" "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-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" 
D34V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      2    1
  2P LOSS WILD-TYPE   22   43
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               2                22
  MALE                 1                43
                   vv
clus                M0 M1 MX
  2P LOSS MUTATED    2  0  1
  2P LOSS WILD-TYPE 43  1 21
D34V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  2P LOSS MUTATED    2  0  1
  2P LOSS WILD-TYPE 44  1 19
D34V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  2P LOSS MUTATED    2  0  0  1
  2P LOSS WILD-TYPE 44  8  1  7
D34V6, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               2                44
  R1               0                 8
  R2               0                 1
  RX               1                 7
D34V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2P LOSS MUTATED         2        1          0          0          0         0
  2P LOSS WILD-TYPE      26       11         13          4          1         1
D34V8, multiclass

Clustering(35) Variable = 2q loss mutation analysis
D35V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED    2  0
  2Q LOSS WILD-TYPE 34 26
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                60 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                26 
$`2Q LOSS MUTATED`
TCGA-BC-A3KF TCGA-DD-A11C 
        0.26        21.44 

$`2Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
        5.03        37.61        13.81         8.28         0.07         4.24 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 
       55.17        37.74        83.57        53.29        22.78         7.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB 
        2.60         0.46        51.25        90.67        79.36        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-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-G3-A25S 
        3.19         0.43        22.85        14.40        19.07         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 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.26              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            21.44             90.67 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            10.85             14.04 
[1] "0.3 - 21.4 (10.9)" "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE"   "2Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                2                60 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113        TCGA-DD-A114 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118        TCGA-DD-A119 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11D        TCGA-DD-A1E9 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-G3-A25S 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25T        TCGA-G3-A25U        TCGA-G3-A25V        TCGA-G3-A25W 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-A25X        TCGA-G3-A25Y        TCGA-G3-A25Z        TCGA-G3-A3CG 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G3-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" 
D35V2, continuous
D35V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      2    2
  2Q LOSS WILD-TYPE   22   42
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               2                22
  MALE                 2                42
                   vv
clus                M0 M1 MX
  2Q LOSS MUTATED    3  0  1
  2Q LOSS WILD-TYPE 42  1 21
D35V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0               3                42
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  2Q LOSS MUTATED    3  0  1
  2Q LOSS WILD-TYPE 43  1 19
D35V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               3                43
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  2Q LOSS MUTATED    2  0  0  2
  2Q LOSS WILD-TYPE 44  8  1  6
D35V6, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               2                44
  R1               0                 8
  R2               0                 1
  RX               2                 6
D35V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  2Q LOSS MUTATED         2        1          1          0          0         0
  2Q LOSS WILD-TYPE      26       11         12          4          1         1
D35V8, multiclass

Clustering(36) Variable = 3p loss mutation analysis
D36V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED    3  2
  3P LOSS WILD-TYPE 33 24
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                5                57 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                2                24 
$`3P LOSS MUTATED`
TCGA-BC-A112 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A118 TCGA-G3-A25T 
        5.03         4.24        55.17        22.78        38.63 

$`3P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A114 
       37.61        13.81         0.26         8.28         0.07        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.29         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-G3-A25S TCGA-G3-A25U TCGA-G3-A25V 
       22.85        14.40        19.07         1.22        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 LOSS MUTATED 3P LOSS WILD-TYPE 
             4.24              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            55.17             90.67 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            22.78             13.81 
[1] "4.2 - 55.2 (22.8)" "0.1 - 90.7 (13.8)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "3P LOSS MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED"   "3P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE"   "3P LOSS MUTATED" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" "3P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D36V2, continuous
D36V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3    2
  3P LOSS WILD-TYPE   21   42
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                21
  MALE                 2                42
                   vv
clus                M0 M1 MX
  3P LOSS MUTATED    4  0  1
  3P LOSS WILD-TYPE 41  1 21
D36V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0               4                41
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  3P LOSS MUTATED    4  0  1
  3P LOSS WILD-TYPE 42  1 19
D36V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               4                42
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  3P LOSS MUTATED    4  0  0  1
  3P LOSS WILD-TYPE 42  8  1  7
D36V6, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               4                42
  R1               0                 8
  R2               0                 1
  RX               1                 7
D36V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3P LOSS MUTATED         1        2          1          0          0         0
  3P LOSS WILD-TYPE      27       10         12          4          1         1
D36V8, multiclass

Clustering(37) Variable = 3q loss mutation analysis
D37V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED    2  1
  3Q LOSS WILD-TYPE 34 25
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                3                59 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                25 
$`3Q LOSS MUTATED`
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-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-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        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 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             5.03              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            55.17             90.67 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            22.78             13.81 
[1] "5.0 - 55.2 (22.8)" "0.1 - 90.7 (13.8)"
       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 MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE"   "3Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D37V2, continuous
D37V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    1
  3Q LOSS WILD-TYPE   22   43
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                22
  MALE                 1                43
                   vv
clus                M0 M1 MX
  3Q LOSS MUTATED    2  0  1
  3Q LOSS WILD-TYPE 43  1 21
D37V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  3Q LOSS MUTATED    2  0  1
  3Q LOSS WILD-TYPE 44  1 19
D37V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               1                19
                   vv
clus                R0 R1 R2 RX
  3Q LOSS MUTATED    3  0  0  0
  3Q LOSS WILD-TYPE 43  8  1  8
D37V6, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               3                43
  R1               0                 8
  R2               0                 1
  RX               0                 8
D37V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  3Q LOSS MUTATED         1        1          0          0          0         0
  3Q LOSS WILD-TYPE      27       11         13          4          1         1
D37V8, multiclass
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                57 
       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-DD-A114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A119        TCGA-DD-A11A 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A11B        TCGA-DD-A11C        TCGA-DD-A11D        TCGA-DD-A1E9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EA        TCGA-DD-A1EB        TCGA-DD-A1EC        TCGA-DD-A1ED 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EE        TCGA-DD-A1EH        TCGA-DD-A1EI        TCGA-DD-A1EJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DD-A1EL        TCGA-EP-A12J        TCGA-EP-A26S        TCGA-EP-A2KA 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-EP-A2KB        TCGA-EP-A2KC        TCGA-EP-A3JL        TCGA-EP-A3RK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-ES-A2HS        TCGA-ES-A2HT        TCGA-FV-A2QR        TCGA-FV-A3I1 
"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(38) Variable = 4p loss mutation analysis
D38V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED    4  4
  4P LOSS WILD-TYPE 32 22
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                8                54 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                4                22 
$`4P LOSS MUTATED`
TCGA-BC-A10Y TCGA-BC-A112 TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25U 
       23.34         5.03        13.64         1.97         1.22        40.47 
TCGA-G3-A25X TCGA-G3-A25Y 
       44.68        14.86 

$`4P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
       27.52         2.99        25.32         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       19.76        53.52         6.67        34.06         6.02        29.16 
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-G3-A25T TCGA-G3-A25V TCGA-G3-A25W 
       22.85        14.40        19.07        38.63        14.27        12.82 
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 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             1.22              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            44.68             90.67 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            14.25             14.04 
[1] "1.2 - 44.7 (14.2)" "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4P LOSS MUTATED" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4P LOSS WILD-TYPE"   "4P LOSS MUTATED" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4P LOSS WILD-TYPE" "4P LOSS WILD-TYPE"   "4P LOSS MUTATED"   "4P LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D38V2, continuous
D38V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      3    6
  4P LOSS WILD-TYPE   21   38
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE               3                21
  MALE                 6                38
                   vv
clus                M0 M1 MX
  4P LOSS MUTATED    6  0  3
  4P LOSS WILD-TYPE 39  1 19
D38V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               6                39
  M1               0                 1
  MX               3                19
                   vv
clus                N0 N1 NX
  4P LOSS MUTATED    6  0  3
  4P LOSS WILD-TYPE 40  1 17
D38V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0               6                40
  N1               0                 1
  NX               3                17
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED    7  1  0  1
  4P LOSS WILD-TYPE 39  7  1  7
D38V6, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0               7                39
  R1               1                 7
  R2               0                 1
  RX               1                 7
D38V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  4P LOSS MUTATED         4        2          1          0          0         0
  4P LOSS WILD-TYPE      24       10         12          4          1         1
D38V8, multiclass

Clustering(39) Variable = 4q loss mutation analysis
D39V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED    8  6
  4Q LOSS WILD-TYPE 28 20
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               14                48 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                6                20 
$`4Q LOSS MUTATED`
TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A112 TCGA-BC-A3KF TCGA-DD-A113 TCGA-DD-A116 
       27.52        23.34         5.03         0.26        55.17        53.29 
TCGA-DD-A11A TCGA-DD-A1EI TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S TCGA-G3-A25X 
        2.60         6.02        13.64         1.97         1.22        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z 
       14.86         8.84 

$`4Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10U 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
        2.99        25.32         1.12        69.57        37.61        13.81 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        8.28         0.07         4.24        37.74        83.57        22.78 
TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-A1EJ 
       66.31        19.76        53.52         6.67        34.06        29.16 
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-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       22.85        14.40        19.07        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       12.82         8.32         6.31         5.88         4.47         0.89 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.26              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            55.17             90.67 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           11.240            14.335 
[1] "0.3 - 55.2 (11.2)" "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "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 MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "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 MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED" "4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"4Q LOSS WILD-TYPE" "4Q LOSS WILD-TYPE"   "4Q LOSS MUTATED"   "4Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-A3CH        TCGA-G3-A3CI 
  "4Q LOSS MUTATED" "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"
D39V2, continuous
D39V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   11
  4Q LOSS WILD-TYPE   19   33
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE               5                19
  MALE                11                33
                   vv
clus                M0 M1 MX
  4Q LOSS MUTATED   11  0  5
  4Q LOSS WILD-TYPE 34  1 17
D39V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0              11                34
  M1               0                 1
  MX               5                17
                   vv
clus                N0 N1 NX
  4Q LOSS MUTATED   11  0  5
  4Q LOSS WILD-TYPE 35  1 15
D39V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              11                35
  N1               0                 1
  NX               5                15
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   13  2  0  1
  4Q LOSS WILD-TYPE 33  6  1  7
D39V6, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              13                33
  R1               2                 6
  R2               0                 1
  RX               1                 7
D39V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  4Q LOSS MUTATED         7        4          2          0          0         0
  4Q LOSS WILD-TYPE      21        8         11          4          1         1
D39V8, multiclass

Clustering(40) Variable = 5q loss mutation analysis
D40V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED    1  3
  5Q LOSS WILD-TYPE 35 23
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                4                58 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                3                23 
$`5Q LOSS MUTATED`
TCGA-BC-A10R TCGA-CC-5263 TCGA-ES-A2HS TCGA-G3-A25S 
       10.13         4.24        22.85         1.22 

$`5Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A113 
       37.61        13.81         0.26         8.28         0.07        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-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-A2KB TCGA-EP-A2KC 
       13.64         4.24         3.62         3.65         1.97         0.62 
TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U 
        3.19         0.43        14.40        19.07        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 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.22              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            22.85             90.67 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            7.185            14.335 
[1] "1.2 - 22.9 (7.2)"  "0.1 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"5Q LOSS WILD-TYPE"   "5Q LOSS MUTATED" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" "5Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D40V2, continuous
D40V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      1    3
  5Q LOSS WILD-TYPE   23   41
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE               1                23
  MALE                 3                41
                   vv
clus                M0 M1 MX
  5Q LOSS MUTATED    2  0  2
  5Q LOSS WILD-TYPE 43  1 20
D40V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               2                43
  M1               0                 1
  MX               2                20
                   vv
clus                N0 N1 NX
  5Q LOSS MUTATED    2  0  2
  5Q LOSS WILD-TYPE 44  1 18
D40V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0               2                44
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED    2  1  0  1
  5Q LOSS WILD-TYPE 44  7  1  7
D40V6, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0               2                44
  R1               1                 7
  R2               0                 1
  RX               1                 7
D40V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  5Q LOSS MUTATED         2        0          1          0          0         0
  5Q LOSS WILD-TYPE      26       12         12          4          1         1
D40V8, multiclass

Clustering(41) Variable = 6q loss mutation analysis
D41V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED    8  2
  6Q LOSS WILD-TYPE 28 24
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                52 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                2                24 
$`6Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-DD-A118 TCGA-DD-A11C TCGA-DD-A1EC TCGA-DD-A1EE TCGA-EP-A12J 
       37.32        22.78        21.44        19.76         6.67         4.24 
TCGA-EP-A3RK TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25X 
        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-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-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED 
        0.46        51.25        90.67        79.36        66.31        53.52 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A26S TCGA-EP-A2KA 
       34.06         6.02        29.16        13.64         3.62         3.65 
TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-G3-A25S 
        1.97         0.62         3.19        22.85        14.40         1.22 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       40.47        14.27        12.82        14.86         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.43              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            44.68             90.67 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            20.60             13.23 
[1] "0.4 - 44.7 (20.6)" "0.1 - 90.7 (13.2)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"6Q LOSS WILD-TYPE" "6Q LOSS WILD-TYPE"   "6Q LOSS MUTATED" "6Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D41V2, continuous
D41V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      5    6
  6Q LOSS WILD-TYPE   19   38
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               5                19
  MALE                 6                38
                   vv
clus                M0 M1 MX
  6Q LOSS MUTATED    8  0  3
  6Q LOSS WILD-TYPE 37  1 19
D41V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               8                37
  M1               0                 1
  MX               3                19
                   vv
clus                N0 N1 NX
  6Q LOSS MUTATED    8  0  3
  6Q LOSS WILD-TYPE 38  1 17
D41V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0               8                38
  N1               0                 1
  NX               3                17
                   vv
clus                R0 R1 R2 RX
  6Q LOSS MUTATED    6  1  0  3
  6Q LOSS WILD-TYPE 40  7  1  5
D41V6, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0               6                40
  R1               1                 7
  R2               0                 1
  RX               3                 5
D41V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  6Q LOSS MUTATED         5        2          2          1          0         0
  6Q LOSS WILD-TYPE      23       10         11          3          1         1
D41V8, multiclass

Clustering(42) Variable = 7p loss mutation analysis
D42V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED    3  0
  7P LOSS WILD-TYPE 33 26
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                3                59 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                0                26 
$`7P LOSS MUTATED`
TCGA-BC-A217 TCGA-BC-A3KG TCGA-EP-A2KB 
       13.81         8.28         1.97 

$`7P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
        5.03        37.61         0.26         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-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-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        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 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.97              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            13.81             90.67 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             8.28             14.40 
[1] "2.0 - 13.8 (8.3)"  "0.1 - 90.7 (14.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7P LOSS MUTATED" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE"   "7P LOSS MUTATED" "7P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" "7P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D42V2, continuous
D42V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      4    1
  7P LOSS WILD-TYPE   20   43
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               4                20
  MALE                 1                43
                   vv
clus                M0 M1 MX
  7P LOSS MUTATED    3  0  2
  7P LOSS WILD-TYPE 42  1 20
D42V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  M0               3                42
  M1               0                 1
  MX               2                20
                   vv
clus                N0 N1 NX
  7P LOSS MUTATED    3  0  2
  7P LOSS WILD-TYPE 43  1 18
D42V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               3                43
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  7P LOSS MUTATED    4  0  0  1
  7P LOSS WILD-TYPE 42  8  1  7
D42V6, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  R0               4                42
  R1               0                 8
  R2               0                 1
  RX               1                 7
D42V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7P LOSS MUTATED         1        4          0          0          0         0
  7P LOSS WILD-TYPE      27        8         13          4          1         1
D42V8, multiclass

Clustering(43) Variable = 7q loss mutation analysis
D43V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED    4  2
  7Q LOSS WILD-TYPE 32 24
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                6                56 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2                24 
$`7Q LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A217 TCGA-BC-A3KG TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25S 
       48.99        13.81         8.28        13.64         1.97         1.22 

$`7Q LOSS WILD-TYPE`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       11.57        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 
        2.99        25.32        23.34         1.12        69.57         5.03 
TCGA-BC-A216 TCGA-BC-A3KF TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
       37.61         0.26         0.07         4.24        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-EP-A12J 
       53.52         6.67        34.06         6.02        29.16         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.62         3.65         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-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 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.22              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            48.99             90.67 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            10.96             14.63 
[1] "1.2 - 49.0 (11.0)" "0.1 - 90.7 (14.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"7Q LOSS WILD-TYPE"   "7Q LOSS MUTATED" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D43V2, continuous
D43V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      4    3
  7Q LOSS WILD-TYPE   20   41
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               4                20
  MALE                 3                41
                   vv
clus                M0 M1 MX
  7Q LOSS MUTATED    6  0  1
  7Q LOSS WILD-TYPE 39  1 21
D43V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0               6                39
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  7Q LOSS MUTATED    5  0  2
  7Q LOSS WILD-TYPE 41  1 18
D43V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               5                41
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  7Q LOSS MUTATED    4  2  0  1
  7Q LOSS WILD-TYPE 42  6  1  7
D43V6, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               4                42
  R1               2                 6
  R2               0                 1
  RX               1                 7
D43V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  7Q LOSS MUTATED         2        4          1          0          0         0
  7Q LOSS WILD-TYPE      26        8         12          4          1         1
D43V8, multiclass

Clustering(44) Variable = 8p loss mutation analysis
D44V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   14 13
  8P LOSS WILD-TYPE 22 13
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               27                35 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               13                13 
$`8P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A216 
       48.99        37.32        10.13        27.52         5.03        37.61 
TCGA-BC-A217 TCGA-BC-A3KG TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
       13.81         8.28        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-DD-A114 
        1.12        69.57         0.26         0.07         4.24        37.74 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        51.25        90.67        79.36 
TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EH TCGA-DD-A1EI TCGA-EP-A12J 
       66.31        19.76        53.52        34.06         6.02         4.24 
TCGA-EP-A2KB TCGA-EP-A3JL TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25X 
        1.97         3.19        38.63        40.47        14.27        44.68 
TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
        8.84         8.32         6.31         5.88         0.89 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.43              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            83.57             90.67 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            14.40             11.57 
[1] "0.4 - 83.6 (14.4)" "0.1 - 90.7 (11.6)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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 MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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 MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED"   "8P LOSS MUTATED"   "8P LOSS MUTATED" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
  "8P LOSS MUTATED"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE" "8P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8P LOSS WILD-TYPE"   "8P LOSS MUTATED" "8P LOSS WILD-TYPE"   "8P LOSS MUTATED" 
       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 MUTATED" "8P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D44V2, continuous
D44V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     13   17
  8P LOSS WILD-TYPE   11   27
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              13                11
  MALE                17                27
                   vv
clus                M0 M1 MX
  8P LOSS MUTATED   19  0 11
  8P LOSS WILD-TYPE 26  1 11
D44V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0              19                26
  M1               0                 1
  MX              11                11
                   vv
clus                N0 N1 NX
  8P LOSS MUTATED   18  1 11
  8P LOSS WILD-TYPE 28  0  9
D44V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              18                28
  N1               1                 0
  NX              11                 9
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   20  4  0  3
  8P LOSS WILD-TYPE 26  4  1  5
D44V6, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              20                26
  R1               4                 4
  R2               0                 1
  RX               3                 5
D44V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8P LOSS MUTATED         9        7          7          2          1         0
  8P LOSS WILD-TYPE      19        5          6          2          0         1
D44V8, multiclass

Clustering(45) Variable = 8q loss mutation analysis
D45V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED    2  2
  8Q LOSS WILD-TYPE 34 24
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                4                58 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                2                24 
$`8Q LOSS MUTATED`
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-DD-A113 TCGA-DD-A114 
       37.61         0.26         0.07         4.24        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-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-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       40.47        14.27        12.82        44.68         8.84         8.32 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        6.31         5.88         4.47         0.89 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             8.28              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            27.52             90.67 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           14.335            13.955 
[1] "8.3 - 27.5 (14.3)" "0.1 - 90.7 (14.0)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
  "8Q LOSS MUTATED" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE"   "8Q LOSS MUTATED" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D45V2, continuous
D45V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      3    2
  8Q LOSS WILD-TYPE   21   42
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               3                21
  MALE                 2                42
                   vv
clus                M0 M1 MX
  8Q LOSS MUTATED    4  0  1
  8Q LOSS WILD-TYPE 41  1 21
D45V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0               4                41
  M1               0                 1
  MX               1                21
                   vv
clus                N0 N1 NX
  8Q LOSS MUTATED    3  0  2
  8Q LOSS WILD-TYPE 43  1 18
D45V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               3                43
  N1               0                 1
  NX               2                18
                   vv
clus                R0 R1 R2 RX
  8Q LOSS MUTATED    3  1  0  1
  8Q LOSS WILD-TYPE 43  7  1  7
D45V6, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               3                43
  R1               1                 7
  R2               0                 1
  RX               1                 7
D45V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  8Q LOSS MUTATED         1        3          0          0          0         0
  8Q LOSS WILD-TYPE      27        9         13          4          1         1
D45V8, multiclass

Clustering(46) Variable = 9p loss mutation analysis
D46V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED    8  7
  9P LOSS WILD-TYPE 28 19
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               15                47 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                7                19 
$`9P LOSS MUTATED`
TCGA-BC-4072 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 
       48.99        10.13        27.52         5.03         0.07        55.17 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EI 
       83.57        53.29         2.60         0.46        21.44         6.02 
TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T 
        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-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11D 
        8.28         4.24        37.74        22.78         7.33        51.25 
TCGA-DD-A1E9 TCGA-DD-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-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 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.26 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            83.57             90.67 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            10.13             14.27 
[1] "0.1 - 83.6 (10.1)" "0.3 - 90.7 (14.3)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE"   "9P LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED"   "9P LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9P LOSS WILD-TYPE"   "9P LOSS MUTATED"   "9P LOSS MUTATED" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" "9P LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"  
D46V2, continuous
D46V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      5   11
  9P LOSS WILD-TYPE   19   33
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               5                19
  MALE                11                33
                   vv
clus                M0 M1 MX
  9P LOSS MUTATED   11  0  5
  9P LOSS WILD-TYPE 34  1 17
D46V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0              11                34
  M1               0                 1
  MX               5                17
                   vv
clus                N0 N1 NX
  9P LOSS MUTATED   12  0  4
  9P LOSS WILD-TYPE 34  1 16
D46V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              12                34
  N1               0                 1
  NX               4                16
                   vv
clus                R0 R1 R2 RX
  9P LOSS MUTATED    9  3  0  3
  9P LOSS WILD-TYPE 37  5  1  5
D46V6, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0               9                37
  R1               3                 5
  R2               0                 1
  RX               3                 5
D46V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9P LOSS MUTATED         5        4          4          0          0         0
  9P LOSS WILD-TYPE      23        8          9          4          1         1
D46V8, multiclass

Clustering(47) Variable = 9q loss mutation analysis
D47V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED    8  5
  9Q LOSS WILD-TYPE 28 21
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               13                49 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                21 
$`9Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A112 TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A116 
       10.13        27.52         5.03         0.07        55.17        53.29 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EI TCGA-EP-A3RK TCGA-G3-A25S 
        2.60         0.46        21.44         6.02         0.43         1.22 
TCGA-G3-A25T 
       38.63 

$`9Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10W 
       48.99        11.57        37.32        46.78        27.52         2.99 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 
       25.32        23.34         1.12        69.57        37.61        13.81 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5263 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 
        0.26         8.28         4.24        37.74        83.57        22.78 
TCGA-DD-A119 TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       14.40        19.07        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.07              0.26 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            55.17             90.67 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             6.02             14.40 
[1] "0.1 - 55.2 (6.0)"  "0.3 - 90.7 (14.4)"
       TCGA-BC-4072        TCGA-BC-4073        TCGA-BC-A10Q        TCGA-BC-A10R 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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 MUTATED" 
       TCGA-BC-A10S        TCGA-BC-A10T        TCGA-BC-A10U        TCGA-BC-A10W 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A10X        TCGA-BC-A10Y        TCGA-BC-A10Z        TCGA-BC-A110 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A112        TCGA-BC-A216        TCGA-BC-A217        TCGA-BC-A3KF 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-BC-A3KG        TCGA-CC-5258        TCGA-CC-5263        TCGA-DD-A113 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" 
       TCGA-DD-A114        TCGA-DD-A115        TCGA-DD-A116        TCGA-DD-A118 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A119        TCGA-DD-A11A        TCGA-DD-A11B        TCGA-DD-A11C 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" 
       TCGA-DD-A11D        TCGA-DD-A1E9        TCGA-DD-A1EA        TCGA-DD-A1EB 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EC        TCGA-DD-A1ED        TCGA-DD-A1EE        TCGA-DD-A1EH 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-DD-A1EI        TCGA-DD-A1EJ        TCGA-DD-A1EL        TCGA-EP-A12J 
  "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A26S        TCGA-EP-A2KA        TCGA-EP-A2KB        TCGA-EP-A2KC 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-EP-A3JL        TCGA-EP-A3RK        TCGA-ES-A2HS        TCGA-ES-A2HT 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-FV-A2QR        TCGA-G3-A25S        TCGA-G3-A25T        TCGA-G3-A25U 
"9Q LOSS WILD-TYPE"   "9Q LOSS MUTATED"   "9Q LOSS MUTATED" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25V        TCGA-G3-A25W        TCGA-G3-A25X        TCGA-G3-A25Y 
"9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" "9Q LOSS WILD-TYPE" 
       TCGA-G3-A25Z        TCGA-G3-A3CG        TCGA-G3-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"
D47V2, continuous
D47V3, binary
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      4   10
  9Q LOSS WILD-TYPE   20   34
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               4                20
  MALE                10                34
                   vv
clus                M0 M1 MX
  9Q LOSS MUTATED    9  0  5
  9Q LOSS WILD-TYPE 36  1 17
D47V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               9                36
  M1               0                 1
  MX               5                17
                   vv
clus                N0 N1 NX
  9Q LOSS MUTATED   10  0  4
  9Q LOSS WILD-TYPE 36  1 16
D47V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              10                36
  N1               0                 1
  NX               4                16
                   vv
clus                R0 R1 R2 RX
  9Q LOSS MUTATED    8  2  0  3
  9Q LOSS WILD-TYPE 38  6  1  5
D47V6, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0               8                38
  R1               2                 6
  R2               0                 1
  RX               3                 5
D47V7, continuous
                   vv
clus                STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC STAGE IVB
  9Q LOSS MUTATED         5        4          2          0          0         0
  9Q LOSS WILD-TYPE      23        8         11          4          1         1
D47V8, multiclass

Clustering(48) Variable = 10p loss mutation analysis
D48V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED    2  1
  10P LOSS WILD-TYPE 34 25
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 3                 59 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 25 
$`10P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A112 TCGA-DD-A11C 
       11.57         5.03        21.44 

$`10P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        37.32        10.13        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        0.46        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-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        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 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              5.03               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             21.44              90.67 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             11.57              14.27 
[1] "5.0 - 21.4 (11.6)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10P LOSS WILD-TYPE"   "10P LOSS MUTATED" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10P LOSS MUTATED" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10P LOSS WILD-TYPE" "10P LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D48V2, continuous
D48V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      0    3
  10P LOSS WILD-TYPE   24   41
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE                0                 24
  MALE                  3                 41
                    vv
clus                 M0 M1 MX
  10P LOSS MUTATED    1  0  2
  10P LOSS WILD-TYPE 44  1 20
D48V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                1                 44
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  10P LOSS MUTATED    2  0  1
  10P LOSS WILD-TYPE 44  1 19
D48V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                1                 19
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED    1  1  0  1
  10P LOSS WILD-TYPE 45  7  1  7
D48V6, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0                1                 45
  R1                1                  7
  R2                0                  1
  RX                1                  7
D48V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  10P LOSS MUTATED         1        0          1          0          0
  10P LOSS WILD-TYPE      27       12         12          4          1
                    vv
clus                 STAGE IVB
  10P LOSS MUTATED           0
  10P LOSS WILD-TYPE         1
D48V8, multiclass
[1] "Remove cluster labels:" "10P LOSS MUTATED"      
clus
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 2                 57 
        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-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-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" 

Clustering(49) Variable = 10q loss mutation analysis
D49V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED    5  5
  10Q LOSS WILD-TYPE 31 21
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                10                 52 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 5                 21 
$`10Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A217 
       11.57        37.32        10.13         2.99         5.03        13.81 
TCGA-DD-A11C TCGA-DD-A1EL TCGA-G3-A25U TCGA-G3-A25X 
       21.44        13.64        40.47        44.68 

$`10Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10X TCGA-BC-A10Y 
       48.99        46.78        27.52        27.52        25.32        23.34 
TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 
        1.12        69.57        37.61         0.26         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        4.24        55.17        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
        7.33         2.60         0.46        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-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S 
        3.19         0.43        22.85        14.40        19.07         1.22 
TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG 
       38.63        14.27        12.82        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 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              2.99               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
             44.68              90.67 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            13.725             14.335 
[1] "3.0 - 44.7 (13.7)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED"   "10Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE"   "10Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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-G3-A25S         TCGA-G3-A25T 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "10Q LOSS MUTATED" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"10Q LOSS WILD-TYPE" "10Q LOSS WILD-TYPE" 
[1] "hr=" "1.8"
D49V2, continuous
D49V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      5    7
  10Q LOSS WILD-TYPE   19   37
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE                5                 19
  MALE                  7                 37
                    vv
clus                 M0 M1 MX
  10Q LOSS MUTATED    7  0  5
  10Q LOSS WILD-TYPE 38  1 17
D49V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                7                 38
  M1                0                  1
  MX                5                 17
                    vv
clus                 N0 N1 NX
  10Q LOSS MUTATED    7  0  5
  10Q LOSS WILD-TYPE 39  1 15
D49V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0                7                 39
  N1                0                  1
  NX                5                 15
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED    6  3  0  2
  10Q LOSS WILD-TYPE 40  5  1  6
D49V6, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0                6                 40
  R1                3                  5
  R2                0                  1
  RX                2                  6
D49V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  10Q LOSS MUTATED         2        3          2          1          0
  10Q LOSS WILD-TYPE      26        9         11          3          1
                    vv
clus                 STAGE IVB
  10Q LOSS MUTATED           0
  10Q LOSS WILD-TYPE         1
D49V8, multiclass

Clustering(50) Variable = 11p loss mutation analysis
D50V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED    2  3
  11P LOSS WILD-TYPE 34 23
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 5                 57 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 3                 23 
$`11P LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-DD-A113 TCGA-DD-A115 
       37.32         5.03        13.81        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-DD-A114 TCGA-DD-A116 
        0.26         8.28         0.07         4.24        37.74        53.29 
TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D 
       22.78         7.33         2.60         0.46        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-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-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-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 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              5.03               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             83.57              90.67 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             37.32              13.64 
[1] "5.0 - 83.6 (37.3)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE"   "11P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"11P LOSS WILD-TYPE"   "11P LOSS MUTATED" "11P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "11P LOSS MUTATED" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11P LOSS WILD-TYPE" "11P LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D50V2, continuous
D50V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      3    2
  11P LOSS WILD-TYPE   21   42
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE                3                 21
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  11P LOSS MUTATED    3  0  2
  11P LOSS WILD-TYPE 42  1 20
D50V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                3                 42
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  11P LOSS MUTATED    2  0  3
  11P LOSS WILD-TYPE 44  1 17
D50V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  11P LOSS MUTATED    4  1  0  0
  11P LOSS WILD-TYPE 42  7  1  8
D50V6, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0                4                 42
  R1                1                  7
  R2                0                  1
  RX                0                  8
D50V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  11P LOSS MUTATED         0        2          1          0          0
  11P LOSS WILD-TYPE      28       10         12          4          1
                    vv
clus                 STAGE IVB
  11P LOSS MUTATED           0
  11P LOSS WILD-TYPE         1
D50V8, multiclass

Clustering(51) Variable = 11q loss mutation analysis
D51V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED    4  3
  11Q LOSS WILD-TYPE 32 23
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 7                 55 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 23 
$`11Q LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A112 TCGA-BC-A217 TCGA-CC-5263 TCGA-DD-A113 
       11.57        37.32         5.03        13.81         4.24        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-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.28         0.07        37.74        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 
        7.33         2.60         0.46        21.44        51.25        90.67 
TCGA-DD-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-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              1.22               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             55.17              90.67 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             11.57              14.40 
[1] "1.2 - 55.2 (11.6)" "0.1 - 90.7 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED"   "11Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "11Q LOSS MUTATED"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-DD-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-G3-A25S         TCGA-G3-A25T 
"11Q LOSS WILD-TYPE"   "11Q LOSS MUTATED" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"11Q LOSS WILD-TYPE" "11Q LOSS WILD-TYPE" 
[1] "hr=" "1.4"
D51V2, continuous
D51V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3    5
  11Q LOSS WILD-TYPE   21   39
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE                3                 21
  MALE                  5                 39
                    vv
clus                 M0 M1 MX
  11Q LOSS MUTATED    5  0  3
  11Q LOSS WILD-TYPE 40  1 19
D51V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                5                 40
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  11Q LOSS MUTATED    5  0  3
  11Q LOSS WILD-TYPE 41  1 17
D51V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0                5                 41
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED    3  3  0  2
  11Q LOSS WILD-TYPE 43  5  1  6
D51V6, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0                3                 43
  R1                3                  5
  R2                0                  1
  RX                2                  6
D51V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  11Q LOSS MUTATED         1        2          3          0          0
  11Q LOSS WILD-TYPE      27       10         10          4          1
                    vv
clus                 STAGE IVB
  11Q LOSS MUTATED           0
  11Q LOSS WILD-TYPE         1
D51V8, multiclass

Clustering(52) Variable = 12p loss mutation analysis
D52V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED    4  0
  12P LOSS WILD-TYPE 32 26
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 4                 58 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 0                 26 
$`12P LOSS MUTATED`
TCGA-BC-A217 TCGA-DD-A1EJ TCGA-G3-A25S TCGA-G3-A25Z 
       13.81        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-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-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-G3-A25T 
        3.19         0.43        22.85        14.40        19.07        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG 
       40.47        14.27        12.82        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 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              1.22               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             29.16              90.67 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            11.325             14.335 
[1] "1.2 - 29.2 (11.3)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"12P LOSS WILD-TYPE"   "12P LOSS MUTATED" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE"   "12P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
[1] "hr="     "2.7e+07"
D52V2, continuous
D52V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    2
  12P LOSS WILD-TYPE   22   42
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                 22
  MALE                  2                 42
                    vv
clus                 M0 M1 MX
  12P LOSS MUTATED    4  0  0
  12P LOSS WILD-TYPE 41  1 22
D52V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                4                 41
  M1                0                  1
  MX                0                 22
                    vv
clus                 N0 N1 NX
  12P LOSS MUTATED    2  1  1
  12P LOSS WILD-TYPE 44  0 19
D52V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                2                 44
  N1                1                  0
  NX                1                 19
                    vv
clus                 R0 R1 R2 RX
  12P LOSS MUTATED    3  1  0  0
  12P LOSS WILD-TYPE 43  7  1  8
D52V6, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0                3                 43
  R1                1                  7
  R2                0                  1
  RX                0                  8
D52V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  12P LOSS MUTATED         2        1          0          0          1
  12P LOSS WILD-TYPE      26       11         13          4          0
                    vv
clus                 STAGE IVB
  12P LOSS MUTATED           0
  12P LOSS WILD-TYPE         1
D52V8, multiclass

Clustering(53) Variable = 13q loss mutation analysis
D53V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   13  6
  13Q LOSS WILD-TYPE 23 20
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                19                 43 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                 20 
$`13Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG 
       37.32        10.13        27.52         5.03        13.81         8.28 
TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A11A 
        0.07        55.17        83.57        53.29        22.78         2.60 
TCGA-DD-A11C TCGA-DD-A1EI TCGA-EP-A3RK TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25X 
       21.44         6.02         0.43         1.22        38.63        44.68 
TCGA-G3-A3CH 
        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-DD-A114 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       37.74         7.33         0.46        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-G3-A25U TCGA-G3-A25V 
        3.19        22.85        14.40        19.07        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       12.82        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.26 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             83.57              90.67 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.81              14.27 
[1] "0.1 - 83.6 (13.8)" "0.3 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "13Q LOSS MUTATED"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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 MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED"   "13Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"13Q LOSS WILD-TYPE"   "13Q LOSS MUTATED" "13Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
[1] "hr=" "1.5"
D53V2, continuous
D53V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      8   15
  13Q LOSS WILD-TYPE   16   29
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                8                 16
  MALE                 15                 29
                    vv
clus                 M0 M1 MX
  13Q LOSS MUTATED   18  0  5
  13Q LOSS WILD-TYPE 27  1 17
D53V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0               18                 27
  M1                0                  1
  MX                5                 17
                    vv
clus                 N0 N1 NX
  13Q LOSS MUTATED   17  0  6
  13Q LOSS WILD-TYPE 29  1 14
D53V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               17                 29
  N1                0                  1
  NX                6                 14
                    vv
clus                 R0 R1 R2 RX
  13Q LOSS MUTATED   13  3  0  5
  13Q LOSS WILD-TYPE 33  5  1  3
D53V6, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0               13                 33
  R1                3                  5
  R2                0                  1
  RX                5                  3
D53V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  13Q LOSS MUTATED         5        7          5          2          0
  13Q LOSS WILD-TYPE      23        5          8          2          1
                    vv
clus                 STAGE IVB
  13Q LOSS MUTATED           0
  13Q LOSS WILD-TYPE         1
D53V8, multiclass

Clustering(54) Variable = 14q loss mutation analysis
D54V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   13  6
  14Q LOSS WILD-TYPE 23 20
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                19                 43 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 6                 20 
$`14Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KF 
       37.32        10.13        27.52         5.03        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-DD-A113 TCGA-DD-A118 TCGA-DD-A11A TCGA-DD-A11C 
        8.28         0.07        55.17        22.78         2.60        21.44 
TCGA-DD-A1E9 TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A2KB TCGA-EP-A3RK TCGA-G3-A25S 
       90.67        29.16        13.64         1.97         0.43         1.22 
TCGA-G3-A3CH 
        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-DD-A114 
       23.34         1.12        69.57        37.61         4.24        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A11D TCGA-DD-A1EA 
       83.57        53.29         7.33         0.46        51.25        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-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        4.24         3.62         3.65         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ 
       44.68        14.86         8.84         8.32         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             90.67              83.57 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             10.13              14.86 
[1] "0.1 - 90.7 (10.1)" "0.5 - 83.6 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-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 MUTATED"   "14Q LOSS MUTATED" 
        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 MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-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 MUTATED"   "14Q LOSS MUTATED" 
        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 MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "14Q LOSS MUTATED"   "14Q LOSS MUTATED"   "14Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" 
        TCGA-DD-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 MUTATED"   "14Q LOSS MUTATED" 
        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 MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
  "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"14Q LOSS WILD-TYPE"   "14Q LOSS MUTATED" "14Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"14Q LOSS WILD-TYPE" "14Q LOSS WILD-TYPE" 
[1] "hr=" "1.3"
D54V2, continuous
D54V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      9   13
  14Q LOSS WILD-TYPE   15   31
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE                9                 15
  MALE                 13                 31
                    vv
clus                 M0 M1 MX
  14Q LOSS MUTATED   16  0  6
  14Q LOSS WILD-TYPE 29  1 16
D54V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0               16                 29
  M1                0                  1
  MX                6                 16
                    vv
clus                 N0 N1 NX
  14Q LOSS MUTATED   13  1  8
  14Q LOSS WILD-TYPE 33  0 12
D54V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               13                 33
  N1                1                  0
  NX                8                 12
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   13  3  0  4
  14Q LOSS WILD-TYPE 33  5  1  4
D54V6, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               13                 33
  R1                3                  5
  R2                0                  1
  RX                4                  4
D54V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  14Q LOSS MUTATED         7        6          4          0          1
  14Q LOSS WILD-TYPE      21        6          9          4          0
                    vv
clus                 STAGE IVB
  14Q LOSS MUTATED           0
  14Q LOSS WILD-TYPE         1
D54V8, multiclass

Clustering(55) Variable = 15q loss mutation analysis
D55V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED    3  3
  15Q LOSS WILD-TYPE 33 23
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 6                 56 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 3                 23 
$`15Q LOSS MUTATED`
TCGA-BC-A112 TCGA-DD-A113 TCGA-DD-A115 TCGA-DD-A1EL TCGA-EP-A2KB TCGA-G3-A25Z 
        5.03        55.17        83.57        13.64         1.97         8.84 

$`15Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 
       27.52         2.99        25.32        23.34         1.12        69.57 
TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 
       37.61        13.81         0.26         8.28         0.07         4.24 
TCGA-DD-A114 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
       37.74        53.29        22.78         7.33         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-EP-A12J 
       53.52         6.67        34.06         6.02        29.16         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS 
        3.62         3.65         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
       14.40        19.07         1.22        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI 
       12.82        44.68        14.86         8.32         6.31         5.88 
TCGA-G3-A3CJ TCGA-G3-A3CK 
        4.47         0.89 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              1.97               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             83.57              90.67 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            11.240             14.335 
[1] "2.0 - 83.6 (11.2)" "0.1 - 90.7 (14.3)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "15Q LOSS MUTATED" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE"   "15Q LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D55V2, continuous
D55V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      2    5
  15Q LOSS WILD-TYPE   22   39
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE                2                 22
  MALE                  5                 39
                    vv
clus                 M0 M1 MX
  15Q LOSS MUTATED    5  0  2
  15Q LOSS WILD-TYPE 40  1 20
D55V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                5                 40
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  15Q LOSS MUTATED    5  0  2
  15Q LOSS WILD-TYPE 41  1 18
D55V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0                5                 41
  N1                0                  1
  NX                2                 18
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED    6  0  0  1
  15Q LOSS WILD-TYPE 40  8  1  7
D55V6, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0                6                 40
  R1                0                  8
  R2                0                  1
  RX                1                  7
D55V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  15Q LOSS MUTATED         2        2          2          0          0
  15Q LOSS WILD-TYPE      26       10         11          4          1
                    vv
clus                 STAGE IVB
  15Q LOSS MUTATED           0
  15Q LOSS WILD-TYPE         1
D55V8, multiclass

Clustering(56) Variable = 16p loss mutation analysis
D56V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED    7  3
  16P LOSS WILD-TYPE 29 23
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                10                 52 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 3                 23 
$`16P LOSS MUTATED`
TCGA-BC-A217 TCGA-CC-5258 TCGA-DD-A11B TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ 
       13.81         0.07         0.46        34.06         6.02        29.16 
TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25X TCGA-G3-A25Y 
        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-DD-A113 
        5.03        37.61         0.26         8.28         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       37.74        83.57        53.29        22.78         7.33         2.60 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-G3-A25S 
        0.62         3.19         0.43        14.40        19.07         1.22 
TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
       38.63        40.47        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 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.26 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             44.68              90.67 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            14.335             13.955 
[1] "0.1 - 44.7 (14.3)" "0.3 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "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 MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "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 MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE"   "16P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "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 MUTATED" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16P LOSS WILD-TYPE"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16P LOSS MUTATED"   "16P LOSS MUTATED" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    9
  16P LOSS WILD-TYPE   19   35
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                5                 19
  MALE                  9                 35
                    vv
clus                 M0 M1 MX
  16P LOSS MUTATED   12  0  2
  16P LOSS WILD-TYPE 33  1 20
D56V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0               12                 33
  M1                0                  1
  MX                2                 20
                    vv
clus                 N0 N1 NX
  16P LOSS MUTATED   10  1  3
  16P LOSS WILD-TYPE 36  0 17
D56V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0               10                 36
  N1                1                  0
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  16P LOSS MUTATED    8  0  0  5
  16P LOSS WILD-TYPE 38  8  1  3
D56V6, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                8                 38
  R1                0                  8
  R2                0                  1
  RX                5                  3
D56V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  16P LOSS MUTATED         5        4          1          3          1
  16P LOSS WILD-TYPE      23        8         12          1          0
                    vv
clus                 STAGE IVB
  16P LOSS MUTATED           0
  16P LOSS WILD-TYPE         1
D56V8, multiclass

Clustering(57) Variable = 16q loss mutation analysis
D57V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   13  7
  16Q LOSS WILD-TYPE 23 19
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                20                 42 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 7                 19 
$`16Q LOSS MUTATED`
TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG TCGA-CC-5258 
       46.78         2.99        37.61        13.81         8.28         0.07 
TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A1EH 
        4.24        55.17        53.29         2.60         0.46        34.06 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-EP-A2KB TCGA-ES-A2HS TCGA-G3-A25U TCGA-G3-A25X 
        6.02        29.16         1.97        22.85        40.47        44.68 
TCGA-G3-A25Y TCGA-G3-A3CH 
       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-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D 
       37.74        83.57        22.78         7.33        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-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-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-A2HT TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25T TCGA-G3-A25V 
        0.43        14.40        19.07         1.22        38.63        14.27 
TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       12.82         8.84         8.32         5.88         4.47         0.89 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.26 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             55.17              90.67 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
            14.335             13.955 
[1] "0.1 - 55.2 (14.3)" "0.3 - 90.7 (14.0)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "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 MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "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 MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED"   "16Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "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 MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-EP-A3RK         TCGA-ES-A2HS         TCGA-ES-A2HT 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
  "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
  "16Q LOSS MUTATED"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"16Q LOSS WILD-TYPE"   "16Q LOSS MUTATED" "16Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"16Q LOSS WILD-TYPE" "16Q LOSS WILD-TYPE" 
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   13
  16Q LOSS WILD-TYPE   15   31
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                9                 15
  MALE                 13                 31
                    vv
clus                 M0 M1 MX
  16Q LOSS MUTATED   18  0  4
  16Q LOSS WILD-TYPE 27  1 18
D57V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0               18                 27
  M1                0                  1
  MX                4                 18
                    vv
clus                 N0 N1 NX
  16Q LOSS MUTATED   15  1  6
  16Q LOSS WILD-TYPE 31  0 14
D57V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0               15                 31
  N1                1                  0
  NX                6                 14
                    vv
clus                 R0 R1 R2 RX
  16Q LOSS MUTATED   16  1  0  5
  16Q LOSS WILD-TYPE 30  7  1  3
D57V6, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               16                 30
  R1                1                  7
  R2                0                  1
  RX                5                  3
D57V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  16Q LOSS MUTATED         7        6          4          2          1
  16Q LOSS WILD-TYPE      21        6          9          2          0
                    vv
clus                 STAGE IVB
  16Q LOSS MUTATED           0
  16Q LOSS WILD-TYPE         1
D57V8, multiclass

Clustering(58) Variable = 17p loss mutation analysis
D58V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   14 12
  17P LOSS WILD-TYPE 22 14
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                26                 36 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                12                 14 
$`17P LOSS MUTATED`
TCGA-BC-4073 TCGA-BC-A10R TCGA-BC-A10U TCGA-BC-A10Z TCGA-BC-A217 TCGA-BC-A3KF 
       11.57        10.13        27.52         1.12        13.81         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 
        8.28         0.07         4.24        83.57        53.29        22.78 
TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EH 
        7.33         2.60        21.44        51.25        66.31        34.06 
TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-EP-A2KC TCGA-FV-A2QR TCGA-G3-A25S TCGA-G3-A25Y 
       29.16        13.64         0.62        19.07         1.22        14.86 
TCGA-G3-A25Z TCGA-G3-A3CH 
        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-DD-A113 TCGA-DD-A114 
       23.34        69.57         5.03        37.61        55.17        37.74 
TCGA-DD-A11B TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EE 
        0.46        90.67        79.36        19.76        53.52         6.67 
TCGA-DD-A1EI TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3JL 
        6.02         4.24         3.62         3.65         1.97         3.19 
TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V 
        0.43        22.85        14.40        38.63        40.47        14.27 
TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A3CG TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
       12.82        44.68         8.32         5.88         4.47         0.89 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.43 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             83.57              90.67 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            12.605             17.080 
[1] "0.1 - 83.6 (12.6)" "0.4 - 90.7 (17.1)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
  "17P LOSS MUTATED" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
  "17P LOSS MUTATED"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1EA         TCGA-DD-A1EB         TCGA-DD-A1EC 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-DD-A1ED         TCGA-DD-A1EE         TCGA-DD-A1EH 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE"   "17P LOSS MUTATED" 
        TCGA-DD-A1EI         TCGA-DD-A1EJ         TCGA-DD-A1EL 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
  "17P LOSS MUTATED"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED"   "17P LOSS MUTATED" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17P LOSS WILD-TYPE"   "17P LOSS MUTATED" "17P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17P LOSS WILD-TYPE" "17P LOSS WILD-TYPE" 
[1] "hr=" "1.6"
D58V2, continuous
D58V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     10   18
  17P LOSS WILD-TYPE   14   26
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               10                 14
  MALE                 18                 26
                    vv
clus                 M0 M1 MX
  17P LOSS MUTATED   22  1  5
  17P LOSS WILD-TYPE 23  0 17
D58V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0               22                 23
  M1                1                  0
  MX                5                 17
                    vv
clus                 N0 N1 NX
  17P LOSS MUTATED   22  1  5
  17P LOSS WILD-TYPE 24  0 15
D58V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               22                 24
  N1                1                  0
  NX                5                 15
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   18  3  1  5
  17P LOSS WILD-TYPE 28  5  0  3
D58V6, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               18                 28
  R1                3                  5
  R2                1                  0
  RX                5                  3
D58V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17P LOSS MUTATED        12        4          6          2          1
  17P LOSS WILD-TYPE      16        8          7          2          0
                    vv
clus                 STAGE IVB
  17P LOSS MUTATED           1
  17P LOSS WILD-TYPE         0
D58V8, multiclass

Clustering(59) Variable = 17q loss mutation analysis
D59V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED    1  2
  17Q LOSS WILD-TYPE 35 24
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 3                 59 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 24 
$`17Q LOSS MUTATED`
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-DD-A113 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A 
       55.17        37.74        83.57        22.78         7.33         2.60 
TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EC 
        0.46        21.44        51.25        90.67        79.36        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-G3-A25S TCGA-G3-A25T 
        0.43        22.85        14.40        19.07         1.22        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 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             10.13               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             66.31              90.67 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             53.29              13.81 
[1] "10.1 - 66.3 (53.3)" "0.1 - 90.7 (13.8)" 
        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 MUTATED" "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-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 MUTATED" "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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"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 MUTATED" "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-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 MUTATED" "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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"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 MUTATED" "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-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 MUTATED" "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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"17Q LOSS WILD-TYPE" "17Q LOSS WILD-TYPE" 
[1] "hr=" "1.2"
D59V2, continuous
D59V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2    1
  17Q LOSS WILD-TYPE   22   43
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE                2                 22
  MALE                  1                 43
                    vv
clus                 M0 M1 MX
  17Q LOSS MUTATED    2  0  1
  17Q LOSS WILD-TYPE 43  1 21
D59V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                2                 43
  M1                0                  1
  MX                1                 21
                    vv
clus                 N0 N1 NX
  17Q LOSS MUTATED    2  0  1
  17Q LOSS WILD-TYPE 44  1 19
D59V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0                2                 44
  N1                0                  1
  NX                1                 19
                    vv
clus                 R0 R1 R2 RX
  17Q LOSS MUTATED    3  0  0  0
  17Q LOSS WILD-TYPE 43  8  1  8
D59V6, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0                3                 43
  R1                0                  8
  R2                0                  1
  RX                0                  8
D59V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  17Q LOSS MUTATED         1        0          1          0          0
  17Q LOSS WILD-TYPE      27       12         12          4          1
                    vv
clus                 STAGE IVB
  17Q LOSS MUTATED           0
  17Q LOSS WILD-TYPE         1
D59V8, multiclass
[1] "Remove cluster labels:" "17Q LOSS MUTATED"      
clus
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 2                 57 
        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-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-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" 

Clustering(60) Variable = 18p loss mutation analysis
D60V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED    3  4
  18P LOSS WILD-TYPE 33 22
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 7                 55 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                 4                 22 
$`18P LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A217 TCGA-DD-A118 TCGA-DD-A11B TCGA-ES-A2HS 
       10.13         5.03        13.81        22.78         0.46        22.85 
TCGA-G3-A25S 
        1.22 

$`18P LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 
        0.26         8.28         0.07         4.24        55.17        37.74 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D 
       83.57        53.29         7.33         2.60        21.44        51.25 
TCGA-DD-A1E9 TCGA-DD-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-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       19.07        38.63        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.46               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             22.85              90.67 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             10.13              14.40 
[1] "0.5 - 22.9 (10.1)" "0.1 - 90.7 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18P LOSS MUTATED" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE"   "18P LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18P LOSS WILD-TYPE"   "18P LOSS MUTATED" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18P LOSS WILD-TYPE" "18P LOSS WILD-TYPE" 
[1] "hr=" "4.5"
D60V2, continuous
D60V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3    4
  18P LOSS WILD-TYPE   21   40
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE                3                 21
  MALE                  4                 40
                    vv
clus                 M0 M1 MX
  18P LOSS MUTATED    4  0  3
  18P LOSS WILD-TYPE 41  1 19
D60V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                4                 41
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  18P LOSS MUTATED    3  0  4
  18P LOSS WILD-TYPE 43  1 16
D60V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0                3                 43
  N1                0                  1
  NX                4                 16
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED    5  1  0  1
  18P LOSS WILD-TYPE 41  7  1  7
D60V6, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0                5                 41
  R1                1                  7
  R2                0                  1
  RX                1                  7
D60V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18P LOSS MUTATED         4        1          0          0          0
  18P LOSS WILD-TYPE      24       11         13          4          1
                    vv
clus                 STAGE IVB
  18P LOSS MUTATED           0
  18P LOSS WILD-TYPE         1
D60V8, multiclass

Clustering(61) Variable = 18q loss mutation analysis
D61V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED    5  4
  18Q LOSS WILD-TYPE 31 22
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 9                 53 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                 4                 22 
$`18Q LOSS MUTATED`
TCGA-BC-A10R TCGA-BC-A112 TCGA-BC-A216 TCGA-BC-A217 TCGA-DD-A118 TCGA-DD-A11A 
       10.13         5.03        37.61        13.81        22.78         2.60 
TCGA-DD-A11B TCGA-ES-A2HS TCGA-G3-A25S 
        0.46        22.85         1.22 

$`18Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U 
       48.99        11.57        37.32        46.78        27.52        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A3KF 
        2.99        25.32        23.34         1.12        69.57         0.26 
TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A115 
        8.28         0.07         4.24        55.17        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA 
       53.29         7.33        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-G3-A25T 
        0.62         3.19         0.43        14.40        19.07        38.63 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
       40.47        14.27        12.82        44.68        14.86         8.84 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        8.32         6.31         5.88         4.47         0.89 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.46               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             37.61              90.67 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             10.13              14.40 
[1] "0.5 - 37.6 (10.1)" "0.1 - 90.7 (14.4)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
  "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "18Q LOSS MUTATED"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED"   "18Q LOSS MUTATED" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"18Q LOSS WILD-TYPE"   "18Q LOSS MUTATED" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"18Q LOSS WILD-TYPE" "18Q LOSS WILD-TYPE" 
[1] "hr=" "2.6"
D61V2, continuous
D61V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      4    5
  18Q LOSS WILD-TYPE   20   39
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE                4                 20
  MALE                  5                 39
                    vv
clus                 M0 M1 MX
  18Q LOSS MUTATED    6  0  3
  18Q LOSS WILD-TYPE 39  1 19
D61V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0                6                 39
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  18Q LOSS MUTATED    4  0  5
  18Q LOSS WILD-TYPE 42  1 15
D61V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0                4                 42
  N1                0                  1
  NX                5                 15
                    vv
clus                 R0 R1 R2 RX
  18Q LOSS MUTATED    7  1  0  1
  18Q LOSS WILD-TYPE 39  7  1  7
D61V6, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0                7                 39
  R1                1                  7
  R2                0                  1
  RX                1                  7
D61V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  18Q LOSS MUTATED         5        1          1          0          0
  18Q LOSS WILD-TYPE      23       11         12          4          1
                    vv
clus                 STAGE IVB
  18Q LOSS MUTATED           0
  18Q LOSS WILD-TYPE         1
D61V8, multiclass

Clustering(62) Variable = 19p loss mutation analysis
D62V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    4  1
  19P LOSS WILD-TYPE 32 25
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 5                 57 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 1                 25 
$`19P LOSS MUTATED`
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-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-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-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL 
       19.76        53.52         6.67        34.06        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-G3-A25T TCGA-G3-A25U 
        0.43        22.85        14.40        19.07        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 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              1.22               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              6.31              90.67 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              2.99              14.86 
[1] "1.2 - 6.3 (3.0)"   "0.1 - 90.7 (14.9)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"19P LOSS WILD-TYPE"   "19P LOSS MUTATED" "19P LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
[1] "hr=" "2.8"
D62V2, continuous
D62V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      0    5
  19P LOSS WILD-TYPE   24   39
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                0                 24
  MALE                  5                 39
                    vv
clus                 M0 M1 MX
  19P LOSS MUTATED    4  0  1
  19P LOSS WILD-TYPE 41  1 21
D62V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                4                 41
  M1                0                  1
  MX                1                 21
                    vv
clus                 N0 N1 NX
  19P LOSS MUTATED    4  0  1
  19P LOSS WILD-TYPE 42  1 19
D62V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                4                 42
  N1                0                  1
  NX                1                 19
                    vv
clus                 R0 R1 R2 RX
  19P LOSS MUTATED    3  2  0  0
  19P LOSS WILD-TYPE 43  6  1  8
D62V6, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0                3                 43
  R1                2                  6
  R2                0                  1
  RX                0                  8
D62V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  19P LOSS MUTATED         3        0          1          0          0
  19P LOSS WILD-TYPE      25       12         12          4          1
                    vv
clus                 STAGE IVB
  19P LOSS MUTATED           0
  19P LOSS WILD-TYPE         1
D62V8, multiclass

Clustering(63) Variable = 21q loss mutation analysis
D63V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED    3  3
  21Q LOSS WILD-TYPE 33 23
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 56 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 3                 23 
$`21Q LOSS MUTATED`
TCGA-BC-A10U TCGA-BC-A112 TCGA-DD-A11A TCGA-DD-A1EL TCGA-EP-A3RK TCGA-G3-A25S 
       27.52         5.03         2.60        13.64         0.43         1.22 

$`21Q LOSS WILD-TYPE`
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T 
       48.99        11.57        37.32        10.13        46.78        27.52 
TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A216 
        2.99        25.32        23.34         1.12        69.57        37.61 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-CC-5258 TCGA-CC-5263 TCGA-DD-A113 
       13.81         0.26         8.28         0.07         4.24        55.17 
TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B 
       37.74        83.57        53.29        22.78         7.33         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-EP-A12J 
       53.52         6.67        34.06         6.02        29.16         4.24 
TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS 
        3.62         3.65         1.97         0.62         3.19        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25T TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W 
       14.40        19.07        38.63        40.47        14.27        12.82 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-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 LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.43               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             27.52              90.67 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             3.815             14.630 
[1] "0.4 - 27.5 (3.8)"  "0.1 - 90.7 (14.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
  "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" 
        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 MUTATED" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-FV-A2QR         TCGA-G3-A25S         TCGA-G3-A25T 
"21Q LOSS WILD-TYPE"   "21Q LOSS MUTATED" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"21Q LOSS WILD-TYPE" "21Q LOSS WILD-TYPE" 
[1] "hr=" "3.8"
D63V2, continuous
D63V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      0    9
  21Q LOSS WILD-TYPE   24   35
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE                0                 24
  MALE                  9                 35
                    vv
clus                 M0 M1 MX
  21Q LOSS MUTATED    6  0  3
  21Q LOSS WILD-TYPE 39  1 19
D63V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                6                 39
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  21Q LOSS MUTATED    6  0  3
  21Q LOSS WILD-TYPE 40  1 17
D63V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0                6                 40
  N1                0                  1
  NX                3                 17
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED    3  2  0  1
  21Q LOSS WILD-TYPE 43  6  1  7
D63V6, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0                3                 43
  R1                2                  6
  R2                0                  1
  RX                1                  7
D63V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  21Q LOSS MUTATED         2        1          3          1          0
  21Q LOSS WILD-TYPE      26       11         10          3          1
                    vv
clus                 STAGE IVB
  21Q LOSS MUTATED           0
  21Q LOSS WILD-TYPE         1
D63V8, multiclass

Clustering(64) Variable = 22q loss mutation analysis
D64V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED    5  2
  22Q LOSS WILD-TYPE 31 24
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 7                 55 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 2                 24 
$`22Q LOSS MUTATED`
TCGA-BC-A10Q TCGA-BC-A10T TCGA-BC-A217 TCGA-DD-A113 TCGA-EP-A2KB TCGA-G3-A25S 
       37.32        27.52        13.81        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-DD-A114 TCGA-DD-A115 
        0.26         8.28         0.07         4.24        37.74        83.57 
TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       53.29        22.78         7.33         2.60         0.46        21.44 
TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-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-A2HS 
        3.62         3.65         0.62         3.19         0.43        22.85 
TCGA-ES-A2HT TCGA-FV-A2QR TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X 
       14.40        19.07        40.47        14.27        12.82        44.68 
TCGA-G3-A25Y TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ 
       14.86         8.84         8.32         6.31         5.88         4.47 
TCGA-G3-A3CK 
        0.89 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              1.22               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             55.17              90.67 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             27.52              13.64 
[1] "1.2 - 55.2 (27.5)" "0.1 - 90.7 (13.6)"
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-4072         TCGA-BC-4073         TCGA-BC-A10Q 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10R         TCGA-BC-A10S         TCGA-BC-A10T 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A10U         TCGA-BC-A10W         TCGA-BC-A10X 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A10Y         TCGA-BC-A10Z         TCGA-BC-A110 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-BC-A112         TCGA-BC-A216         TCGA-BC-A217 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" 
        TCGA-BC-A3KF         TCGA-BC-A3KG         TCGA-CC-5258 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-CC-5263         TCGA-DD-A113         TCGA-DD-A114 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A115         TCGA-DD-A116         TCGA-DD-A118 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A119         TCGA-DD-A11A         TCGA-DD-A11B 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-A11C         TCGA-DD-A11D         TCGA-DD-A1E9 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-DD-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 MUTATED" "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-G3-A25S         TCGA-G3-A25T 
"22Q LOSS WILD-TYPE"   "22Q LOSS MUTATED"   "22Q LOSS MUTATED" 
        TCGA-G3-A25U         TCGA-G3-A25V         TCGA-G3-A25W 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A25X         TCGA-G3-A25Y         TCGA-G3-A25Z 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CG         TCGA-G3-A3CH         TCGA-G3-A3CI 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
        TCGA-G3-A3CJ         TCGA-G3-A3CK 
"22Q LOSS WILD-TYPE" "22Q LOSS WILD-TYPE" 
[1] "hr=" "1.7"
D64V2, continuous
D64V3, binary
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      6    3
  22Q LOSS WILD-TYPE   18   41
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE                6                 18
  MALE                  3                 41
                    vv
clus                 M0 M1 MX
  22Q LOSS MUTATED    6  0  3
  22Q LOSS WILD-TYPE 39  1 19
D64V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                6                 39
  M1                0                  1
  MX                3                 19
                    vv
clus                 N0 N1 NX
  22Q LOSS MUTATED    5  0  4
  22Q LOSS WILD-TYPE 41  1 16
D64V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0                5                 41
  N1                0                  1
  NX                4                 16
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED    4  3  0  2
  22Q LOSS WILD-TYPE 42  5  1  6
D64V6, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0                4                 42
  R1                3                  5
  R2                0                  1
  RX                2                  6
D64V7, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIIA STAGE IIIB STAGE IIIC
  22Q LOSS MUTATED         2        3          1          1          0
  22Q LOSS WILD-TYPE      26        9         12          3          1
                    vv
clus                 STAGE IVB
  22Q LOSS MUTATED           0
  22Q LOSS WILD-TYPE         1
D64V8, 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")
